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Статті в журналах з теми "Rational enzyme engineering"
Eijsink, Vincent G. H., Alexandra Bjørk, Sigrid Gåseidnes, Reidun Sirevåg, Bjørnar Synstad, Bertus van den Burg, and Gert Vriend. "Rational engineering of enzyme stability." Journal of Biotechnology 113, no. 1-3 (September 2004): 105–20. http://dx.doi.org/10.1016/j.jbiotec.2004.03.026.
Повний текст джерелаMirzaei, Mitra, та Per Berglund. "Engineering of ωTransaminase for Effective Production of Chiral Amines". Journal of Computational and Theoretical Nanoscience 17, № 6 (1 червня 2020): 2827–32. http://dx.doi.org/10.1166/jctn.2020.8947.
Повний текст джерелаChen, Ridong. "Enzyme engineering: rational redesign versus directed evolution." Trends in Biotechnology 19, no. 1 (January 2001): 13–14. http://dx.doi.org/10.1016/s0167-7799(00)01522-5.
Повний текст джерелаAcebes, Sandra, Elena Fernandez-Fueyo, Emanuele Monza, M. Fatima Lucas, David Almendral, Francisco J. Ruiz-Dueñas, Henrik Lund, Angel T. Martinez, and Victor Guallar. "Rational Enzyme Engineering Through Biophysical and Biochemical Modeling." ACS Catalysis 6, no. 3 (February 5, 2016): 1624–29. http://dx.doi.org/10.1021/acscatal.6b00028.
Повний текст джерелаSteiner, Kerstin, and Helmut Schwab. "RECENT ADVANCES IN RATIONAL APPROACHES FOR ENZYME ENGINEERING." Computational and Structural Biotechnology Journal 2, no. 3 (September 2012): e201209010. http://dx.doi.org/10.5936/csbj.201209010.
Повний текст джерелаSousa, João P. M., Pedro Ferreira, Rui P. P. Neves, Maria J. Ramos, and Pedro A. Fernandes. "The bacterial 4S pathway – an economical alternative for crude oil desulphurization that reduces CO2 emissions." Green Chemistry 22, no. 22 (2020): 7604–21. http://dx.doi.org/10.1039/d0gc02055a.
Повний текст джерелаRussell, Alan J., and Alan R. Fersht. "Rational modification of enzyme catalysis by engineering surface charge." Nature 328, no. 6130 (August 1987): 496–500. http://dx.doi.org/10.1038/328496a0.
Повний текст джерелаPayongsri, Panwajee, David Steadman, John Strafford, Andrew MacMurray, Helen C. Hailes, and Paul A. Dalby. "Rational substrate and enzyme engineering of transketolase for aromatics." Organic & Biomolecular Chemistry 10, no. 45 (2012): 9021. http://dx.doi.org/10.1039/c2ob25751c.
Повний текст джерелаYang, Jae-Seong, Sang Woo Seo, Sungho Jang, Gyoo Yeol Jung, and Sanguk Kim. "Rational Engineering of Enzyme Allosteric Regulation through Sequence Evolution Analysis." PLoS Computational Biology 8, no. 7 (July 12, 2012): e1002612. http://dx.doi.org/10.1371/journal.pcbi.1002612.
Повний текст джерелаAlbenne, Cécile, Bart A. Van Der Veen, Gabrielle Potocki-Véronèse, Gilles Joucla, Lars Skov, Osman Mirza, Michael Gajhede, Pierre Monsan, and Magali Remaud-Simeon. "Rational and Combinatorial Engineering of the Glucan Synthesizing Enzyme Amylosucrase." Biocatalysis and Biotransformation 21, no. 4-5 (October 2003): 271–77. http://dx.doi.org/10.1080/10242420310001618537.
Повний текст джерелаДисертації з теми "Rational enzyme engineering"
Knapic, Lorena. "Computational methods for rational screening and engineering of enzyme properties." Doctoral thesis, Università degli studi di Trieste, 2012. http://hdl.handle.net/10077/7388.
Повний текст джерелаState of the art computational thechniques were applied to several current research toppics in biocatalysis such as substrate promiscuity, reaction promiscuity and high throughput mutant generation and screening. The studied subjects are of great interest to industrial biocatalysis nowadays and can find large application for rational redesign of inefficient biocatalysts and fast substrate engineering and screening. The overall work can be devided into three principal areas, i.e. understanding catalytic mechanisms, description of enzyme-substrate interactions and integration of available computational methods for the development of a novel authomatized tool for enzyme engineering. In each of these areas, the goal has been to test the existing methodologies as well as the development of new descriptors and ready to use strategies.
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Acebes, Serrano Sandra. "Rational enzyme engineering of heme peroxidases through biophysical and biochemical modeling." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/399735.
Повний текст джерелаLas enzimas son proteínas que catalizan reacciones bioquímicas y cuyo uso aporta múltiples ventajas, ya que son en general muy selectivas, poco contaminantes (biodegradables), baratas y permiten trabajar en condiciones suaves, en comparación con los procesos tradicionales no enzimáticos. A pesar de sus enormes beneficios, sus aplicaciones a nivel industrial son todavía limitadas, debido principalmente a la baja productividad, baja tolerancia al sustrato (demasiado específicos) y una escasa resistencia a las condiciones industriales en general, y por esta razón el desarrollo de enzimas mejoradas es un campo de investigación muy importante hoy en día. En particular, la aplicación de la química computacional en el campo de la ingeniería de enzimas está en aumento debido a las mejoras en hardware y software. Motivado por este progreso, el objetivo principal de esta tesis es el desarrollo de estrategias de cálculo que, mediante la combinación de diferentes metodologías in silico permitan diseñar y evaluar modificaciones en las enzimas, centrándonos en la obtención de resultados de forma rápida y económica. La primera parte de la tesis está centrada en la descripción del mecanismo enzimático entendido como un proceso de dos pasos que incluyen la difusión ligando y la reacción química, mediante una combinación de diferentes técnicas computacionales. El primer paso, que implica el reconocimiento de la proteína / ligando, se caracterizó con diferentes técnicas basadas en la mecánica molecular (dinámica molecular, docking y Monte Carlo- PELE). Por otro lado, la reacción química (incluyendo la formación de enlaces y la transferencia de electrones) se simuló usando métodos basados en mecánica cuántica por medio de cálculos de energía, la caracterización del spin o cálculos de acoplamiento electrónico. Por ejemplo, siguiendo este procedimiento, se caracterizó la oxidación de alcohol veratrílico por medio de la enzima lignin peroxidasa. Además, con el objetivo de poder calcular los acoplamientos electrónicos de una manera más rápida y fácil, se desarrolló un servidor web: ecoupling server. En la segunda parte de la tesis, los resultados demostraron que el protocolo anterior podría describir funciones enzimáticas no sólo en las especies nativas sino también en las variantes mutadas. Por ejemplo, se identificaron las implicaciones estructurales de la reactividad en una manganeso peroxidasa de la subfamilia larga y su variante modificada obtenida mediante la reducción de los últimos residuos terminales gracias al estudio de simulaciones de Monte Carlo (PELE) y cálculos de acoplamiento electrónico. Además, la resistencia a pH ácido en el mutante 2-1B (que se había obtenido previamente por evolución dirigida al azar) se comparó con la especie nativa y también se racionalizó por dinámica molecular, donde se observó que los residuos del entorno del hemo presentaban diferente conformación debido a las mutaciones introducidas, resultando en una diferente resistencia a pH ácido. La última parte de la tesis se centra en la ingeniería racional de hemo peroxidasas. A partir de predicciones in silico se diseñaron variantes de peroxidasa versátil para tratar de entender los procesos de transferencia electrónica de largo alcance que participan en la oxidación del sustrato de alcohol veratrílico, mediante la identificación de los residuos intermedios involucrados en el proceso. Además, a partir de un estudio computacional completo, se diseñó un mutante mejorado de manganeso peroxidasa, cuyos valores cinéticos estimados computacionalmente se encontraban de acuerdo con los resultados experimentales. En conclusión, en esta tesis se ilustra cómo los métodos biofísicos y bioquímicos computacionales son herramientas prometedoras y valiosas para la ingeniería de enzimas, en particular en el campo del diseño racional.
Hendil-Forssell, Peter. "Rational engineering of esterases for improved amidase specificity in amide synthesis and hydrolysis." Doctoral thesis, KTH, Industriell bioteknologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-196892.
Повний текст джерелаQC 20161125
Sandström, Anders G. "Protein Engineering of Candida antarctica Lipase A : Enhancing Enzyme Properties by Evolutionary and Semi-Rational Methods." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-49248.
Повний текст джерелаAt the time of the doctoral defence the following paper was unpublished and had a status as follows: Paper nr. 5: Manuscript
Gullfot, Fredrika. "On the engineering of proteins: methods and applications for carbohydrate-active enzymes." Doctoral thesis, KTH, Glykovetenskap, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-24296.
Повний текст джерелаQC 20100902
Salin, M. (Mikko). "Protein crystallographic studies of A-TIM—structure based development of new enzymes." Doctoral thesis, University of Oulu, 2010. http://urn.fi/urn:isbn:9789514261237.
Повний текст джерелаTiivistelmä Entsyymit voivat toimia ylivoimaisina katalyytteinä monissa kemianteollisuuden prosesseissa johtuen niiden hyvästä spesifisyydestä, valikoimiskyvystä, alhaisesta energiantarpeesta ja ympäristöystävällisyydestä. Näistä ominaisuuksista huolimatta entsyymien kaikkien mahdollisuuksien hyödyntämisen esteenä on monia haasteita. Tarvittavia ominaisuuksia ovat katalyyttinen tehokkuus, saatavuus suurina määrinä, alhainen hinta, alhainen tuoteinhibitio sekä korkea aktiivisuus ja stabiilisuus prosessiolosuhteissa. TIM-tynnyrirakenne on yleisin ja monipuolisin proteiinien laskostumisrakenne luonnossa esiintyvissä entsyymeissä. Tässä rakenteessa katalyyttisesti aktiiviset aminohappotähteet ovat sijoittuneet tynnyrirakenteen toiselle puolelle, kun taas stabiilisuuden kannalta tärkeät aminohappotähteet ovat sijoittuneet kokonaan toiselle puolelle. Tämä erityinen rakenne antaa mahdollisuuden muokata proteiinin katalyyttistä aktiivisuutta vaikuttamatta haitallisesti sen stabiilisuuteen. Tämä on täydellinen lähtökohta proteiininmuokkaukselle. Tässä tutkimusprojektissa käytettiin ns. järkiperäistä suunnittelua monomeerisen trioosifosfaatti-isomeraasivariantin (A-TIM) luomisessa. Tämän tutkimustyön pääasialliset tavoitteet olivat (i) uusien sitoutujien löytäminen ja (ii) uuden, suuremman sitoutumistaskun ominaisuuksien määrittäminen röntgenkristallografisilla menetelmillä. Tässä tutkimuksessa havaittiin, että A-TIM kykenee sitomaan yhdisteitä, jotka ovat täysin erilaisia luonnolliseen substraattiin verrattuna. Tässä tutkimuksessa kuvaillaan kolmenlaisia sitoutujia: (i) todelliset villityypin entsyymin substraattianalogit, (ii) substraattianalogit, joihin on liitetty hydrofobinen hiilivetyketju ja (iii) villityypin substraattia suuremmat sokerifosfaatit. Tämän lisäksi A-TIM:n aktiivisen keskuksen todistettiin olevan toimintakykyinen. Yleisellä tasolla tämä tutkimus osoittaa röntgenkristallografisten menetelmien tärkeyden entsyymienmuokkausprojekteissa, joissa entsyymivarianttien ominaisuuksien määritys on tärkeää
Modén, Olof. "Mutational Analysis and Redesign of Alpha-class Glutathione Transferases for Enhanced Azathioprine Activity." Doctoral thesis, Uppsala universitet, Biokemi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-167332.
Повний текст джерелаAndrews, Simon Richard. "Alteration of the properties of enzymes by random mutagenesis and rational design." Thesis, University of Newcastle Upon Tyne, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.311165.
Повний текст джерелаBissaro, Bastien. "On hydrolysis / transglycosylation modulation in glycoside hydrolases : lessons learnt from the molecular design of the first non-Leloir transarabinofuranosylases." Thesis, Toulouse, INSA, 2014. http://www.theses.fr/2014ISAT0023/document.
Повний текст джерелаWidening the spectrum of available compounds in the field of Glycosciences is of utmost importance for the entire biology community, because carbohydrates are determinants of a myriad of life-sustaining or threatening processes. The assembly, modification or deconstruction of complex carbohydrate-based structures mainly involves the action of enzymes, among which one can identify Carbohydrate Active enZymes (CAZymes). These enzymes form part of the CAZy database repertoire and include Glycoside Hydrolases (GHs), which are the biggest group of CAZymes, whose main role is to hydrolyze glycosidic linkages. However, some GHs also display the ability to perform synthesis (transglycosylation), an activity that mostly manifests itself as a minor one alongside hydrolysis, but which is the only activity displayed by a rather select group of GHs that are often called transglycosylases. Understanding how transglycosylases have resulted from the process of evolution is both intringuing and crucial, because it holds the key to the creation of tailored glycosynthetic enzymes that will revolutionize the field of glycosciences.In this thesis, an extensive review of relevant scientific literature that treats the different aspects of GH-catalyzed transglycosylation and glycosynthesis is presented, along with experimental results of work that has been performed on a family GH-51 α-L-arabinofuranosidase, a pentose-acting enzyme from Thermobacillus xylanilyticus (TxAbf). The conclusions of the literature are presented in the form of a hypothesis, which describes the molecular basis of the hydrolysis/transglycosylation partition and thus provides a proposal on how to engineer dominant transglycosylation activity in a GH. Afterwards, using a directed evolution approach, including random mutagenesis, semi-rational approaches, in silico predictions and recombination it has been experimentally possible to create the very first ‘non-Leloir’ transarabinofuranosylases. The mechanistic analysis of the resultant TxAbf mutants notably focusing on the hydrolysis/transglycosylation partition reveals that the results obtained are consistent with the initial hypothesis that was formulated on the basis of the literature review.To demonstrate the applicative value of the experimental work performed in this study, the TxAbf mutants were used to develop a chemo-enzymatic methodology that has procured a panel of well-defined furanosylated compounds. Enzyme-catalyzed transfer of arabinofuranosyl moities can be used to generate arabinoxylo-oligosaccharides (AXOS), but the design of non-natural oligosaccharides, such as galactofuranoxylo-oligosaccharides or arabinofuranogluco-oligosaccharides is also possible. Overall, the work presented constitutes the first steps towards the development of more sophiscated methodologies that will procure the means to synthesize artificial arabinoxylans, with a first proof of concept being presented at the very end of this manuscript.In the present context of the bioeconomy transition, which relies on technologies such as biorefining and green chemistry, it is expected that the glycosynthetic tools that have been developed in this work will be useful for the conversion of pentose sugars obtained from biomass. The synthesis of tailor-made arabinoxylo-oligo- and polysaccharides may lead to a variety of potential applications including the production of prebiotics, surfactants or bio-inspired materials and, more fundamentally, the synthesis of artificial models of plant cell wall
Rajado, Ana Teresa Amado Mateus Santos. "Computation meets experimentation to improve the catatysis and specificity of Cas12a genome editing enzyme." Master's thesis, 2020. http://hdl.handle.net/10316/92173.
Повний текст джерелаO sistema CRISPR-Cas é uma ferramenta aplicada a edição genética. Esta técnica tornou-se altamente relevante nos últimos anos devido ao seu baixo custo e facilidade de produção e utilização.Cas12a é uma endonuclease do tipo V do Sistema CRISPR-Cas, capaz de editar genoma humano recorrendo a um único RNA guia. Esta enzima já foi adaptada e utilizada em diversas áreas, tal como medicina e agricultura, através da edição genética de células de diferentes tipos, como por exemplo células animais e vegetais. No entanto, este sistema também enfrenta alguns problemas, dos quais se destacam as mutações introduzidas fora dos locais alvo (“off-target mutations”), que são introduzidas de forma não intencional.O objetivo deste trabalho é estudar o mecanismo catalítico da enzima Cas12a, com o intuito de aumentar a especificidade do mesmo. Com este propósito recorremos a uma combinação de métodos computacionais (Dinâmica Molecular) e experimentais (Biologia Molecular), para reduzir os efeitos “off-target” acima mencionados.Foram estudadas seis variantes da enzima nativa (direcionadas para as regiões da enzima que interagem com o motivo PAM, com o loop no terminal 5’ do crRNA e com o centro ativo da enzima) e dois estados intermediários do ciclo catalítico da mesma. Com as variantes criadas induzimos interações mais fortes do que as previamente presentes entre a FnCas12a, uma enzima para edição genética, e o crRNA e DNA alvo a ela associados. Substituímos resíduos polares e não polares por lisinas, carregadas positivamente, criando interações carga-carga com o DNA e o crRNA, o que poderá conduzir ao reconhecimento específico entre a proteína e os ácidos nucleicos através de um mecanismo de reconhecimento indireto (indirect readout mechanism), uma vez que os resíduos mutados não interagem com as bases azotadas.Explorámos também o mecanismo catalítico desta enzima, ao estudarmos a relevância dos resíduos H922 e R1218, localizados no local catalítico da enzima. De acordo com as nossas simulações, H922 aparenta ser o resíduo que atua como base catalítica através de um mecanismo concertado. Neste, a histidina deverá receber um protão da água enquanto que ao mesmo tempo esta realiza um ataque nucleofílico ao grupo fosfato em que irá ocorrer a clivagem.
The CRISPR-Cas system is a tool used for genome editing that became highly relevant in the latest years for being cheap, easy to design and produce.Cas12a is an endonuclease type V of the CRISPR-Cas system and is able to edit human genome through a single-RNA guided approach. This enzyme has already been repurposed to be applied in several fields, such as in medicine and agriculture, through the genome editing of different cells types such animal and plant cell. However a recurrent problem of these systems and related ones is the off-target mutations - unintentionally induced.The objective of this work is to study Cas12a enzyme. For this, we used a combination of computational (Molecular Dynamics) and experimental (Molecular Biology) methods, in order to surpass the above mentioned obstacles.Six variants of the wild type enzyme (directed to enzyme’ regions that interact with the PAM motif, the crRNA 5’ handle and with the active site of the protein) and two putative intermediates of its catalytic cycle were tested. With these variants, we induced stronger interactions between FnCas12a, a genome editing enzyme, and its crRNA and target DNA. We have substituted polar and non-polar residues with positively charged lysine residues creating new salt-bridges with the cRNA and DNA and possibly leading to specific recognition through an indirect readout mechanism, since the newly introduced residues do not interact with the bases.Additionally, we explored the catalytic mechanism of this enzyme, by studying the relevance of H922 and R1218, residues located in the catalytic site of the enzyme. According to our simulations, H922 seems to be the most probable residue to act as a base through a concerted mechanism, in which it receives a proton from the water, simultaneously with nucleophilic attack on the phosphate group that is going to be cleaved.
Книги з теми "Rational enzyme engineering"
Kumar, C. Vijay. Rational Design of Enzyme-Nanomaterials. Elsevier Science & Technology, 2016.
Знайти повний текст джерелаЧастини книг з теми "Rational enzyme engineering"
Pongsupasa, Vinutsada, Piyanuch Anuwan, Somchart Maenpuen, and Thanyaporn Wongnate. "Rational-Design Engineering to Improve Enzyme Thermostability." In Methods in Molecular Biology, 159–78. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1826-4_9.
Повний текст джерелаShivange, Amol V., and Ulrich Schwaneberg. "Recent Advances in Directed Phytase Evolution and Rational Phytase Engineering." In Directed Enzyme Evolution: Advances and Applications, 145–72. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-50413-1_6.
Повний текст джерелаLee, Charles K., Colin R. Monk, and Roy M. Daniel. "Determination of Enzyme Thermal Parameters for Rational Enzyme Engineering and Environmental/Evolutionary Studies." In Methods in Molecular Biology, 219–30. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-354-1_13.
Повний текст джерелаWeiland, Mitch H. "Enzymatic Biodegradation by Exploring the Rational Protein Engineering of the Polyethylene Terephthalate Hydrolyzing Enzyme PETase from Ideonella sakaiensis 201-F6." In ACS Symposium Series, 161–74. Washington, DC: American Chemical Society, 2020. http://dx.doi.org/10.1021/bk-2020-1357.ch008.
Повний текст джерелаBraco, Lorenzo, and Ismael Mingarro. "Interfacial Activation-Based Molecular Bioimprinting: Towards a More Rational Use of Lipolytic Enzymes in Nonaqueous Media." In Engineering of/with Lipases, 229–42. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-1671-5_15.
Повний текст джерелаLi, Danyang, Qi Wu, and Manfred T. Reetz. "Focused rational iterative site-specific mutagenesis (FRISM)." In Enzyme Engineering and Evolution: General Methods, 225–42. Elsevier, 2020. http://dx.doi.org/10.1016/bs.mie.2020.04.055.
Повний текст джерелаChoi, Jung Min, and Hak-Sung Kim. "Structure-guided rational design of the substrate specificity and catalytic activity of an enzyme." In Enzyme Engineering and Evolution: General Methods, 181–202. Elsevier, 2020. http://dx.doi.org/10.1016/bs.mie.2020.04.050.
Повний текст джерелаAnand, Swadha, and Debasisa Mohanty. "Computational Methods for Identification of Novel Secondary Metabolite Biosynthetic Pathways by Genome Analysis." In Handbook of Research on Computational and Systems Biology, 380–405. IGI Global, 2011. http://dx.doi.org/10.4018/978-1-60960-491-2.ch018.
Повний текст джерела