Structure Dynamics Guided Enzyme Improvement of ENDO-BETA-1, 4-XYLANASE I PDF Download
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Author: Ugur Uzuner
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Enzyme structure dynamics has recently been revealed to be essential for structure-function relationship. Among various structure dynamics analysis platforms, hydrogen deuterium exchange mass spectrometry stands as an efficient and high-throughput way to analyze protein dynamics upon ligand binding, protein folding, and enzyme catalysis. HDX-MS can be used to study the regional dynamics of proteins based on the m/z value or percentage of deuterium incorporation for the digested peptides in the HDX experiments. Various software packages have been developed to analyze HDX-MS data. However, for the accurate, enhanced, and explicit statistical analysis of HDX-MS data statistical analysis of software was developed as HDXanalyzer. The capability of HDX-MS analysis for the identification of enzyme structure dynamics was tested by using model catalysis endoxylanase A (XYN I) from Trichoderma longibrachiatum. The HDX data of XYN I revealed a highly dynamic personality of XYN I through the interaction with two substrates. The dynamic data which certainly restricts the targeted regions for the protein engineering efforts provided useful knowledge about the essential structural modifications for the catalysis of XYN I. The obtained knowledge was then employed for the engineering studies in order to improve the certain characteristics of XYN I protein. The high level stabilization of XYN I protein was gathered and the two highly active and moderately thermostable XYN I recombinants were developed based on the HDX-MS data which further confirmed the efficiency of the current strategy for the rational designs of catalytic proteins. A differential dynamics analysis of the two structurally similar catalysts was also performed through HDX-MS. The functionally and sequentially different but structurally highly similar XYN I and endoglucanase (Eg1A) enzymes revealed distinct structure dynamic characteristics. Compared to XYN I, Eg1A from Aspergillus niger indicated quite restricted structural motions. The data clearly postulated that the intrinsic dynamic modifications of during the enzymatic catalysis may not be the only driving force in all cases. In summary, the integration of the structure dynamics knowledge to the current biochemical and biophysical data of catalysts may provide novel insights to further enzyme improvement applications. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/150988
Author: Ugur Uzuner
Publisher:
ISBN:
Category :
Languages : en
Pages :
Get Book Here
Book Description
Enzyme structure dynamics has recently been revealed to be essential for structure-function relationship. Among various structure dynamics analysis platforms, hydrogen deuterium exchange mass spectrometry stands as an efficient and high-throughput way to analyze protein dynamics upon ligand binding, protein folding, and enzyme catalysis. HDX-MS can be used to study the regional dynamics of proteins based on the m/z value or percentage of deuterium incorporation for the digested peptides in the HDX experiments. Various software packages have been developed to analyze HDX-MS data. However, for the accurate, enhanced, and explicit statistical analysis of HDX-MS data statistical analysis of software was developed as HDXanalyzer. The capability of HDX-MS analysis for the identification of enzyme structure dynamics was tested by using model catalysis endoxylanase A (XYN I) from Trichoderma longibrachiatum. The HDX data of XYN I revealed a highly dynamic personality of XYN I through the interaction with two substrates. The dynamic data which certainly restricts the targeted regions for the protein engineering efforts provided useful knowledge about the essential structural modifications for the catalysis of XYN I. The obtained knowledge was then employed for the engineering studies in order to improve the certain characteristics of XYN I protein. The high level stabilization of XYN I protein was gathered and the two highly active and moderately thermostable XYN I recombinants were developed based on the HDX-MS data which further confirmed the efficiency of the current strategy for the rational designs of catalytic proteins. A differential dynamics analysis of the two structurally similar catalysts was also performed through HDX-MS. The functionally and sequentially different but structurally highly similar XYN I and endoglucanase (Eg1A) enzymes revealed distinct structure dynamic characteristics. Compared to XYN I, Eg1A from Aspergillus niger indicated quite restricted structural motions. The data clearly postulated that the intrinsic dynamic modifications of during the enzymatic catalysis may not be the only driving force in all cases. In summary, the integration of the structure dynamics knowledge to the current biochemical and biophysical data of catalysts may provide novel insights to further enzyme improvement applications. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/150988
Author: Stephan A. Sieber
Publisher: Springer Science & Business Media
ISBN: 3642283780
Category : Science
Languages : en
Pages : 175
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Book Description
ABPP Methodology: Introduction and Overview, by Matthew B. Nodwell und Stephan A. Sieber Activity-Based Protein Profiling for Natural Product Target Discovery, by Joanna Krysiak und Rolf Breinbauer Photoaffinity Labeling in Activity-Based Protein Profiling, by Paul P. Geurink, Laurette M. Prely, Gijs A. van der Marel, Rainer Bischoff und Herman S. Overkleeft Application of Activity-Based Protein Profiling to the Study of Microbial Pathogenesis, by William P. Heal und Edward W. Tate Functional Analysis of Protein Targets by Metabolomic Approaches, by Yun-Gon Kim und Alan Saghatelian
Author: Peter Grunwald
Publisher: World Scientific Publishing Company
ISBN: 1783269103
Category : Science
Languages : en
Pages : 1314
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Book Description
In this Completely Revised and Extended Edition with a significantly enhanced content, all Chapters have been updated considering relevant literature and recent developments until 2016 together with application oriented examples with a focus on Industrial Biocatalysis. Newly treated topics comprise among others systems metabolic engineering approaches, metagenome screening, new tools for pathway engineering, and de-novo computational design as actual research areas in biocatalysis. Information about different aspects of RNA technologies, and completely new Chapters on 'Fluorescent Proteins' and 'Biocatalysis and Nanotechnology' are also included.
Author: Prashant Kumar Singh
Publisher: Frontiers Media SA
ISBN: 2832551114
Category : Science
Languages : en
Pages : 184
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Book Description
Scientific research on cold-adapted microorganisms (specifically polar microbes) is of great interest, since Arctic and Antarctic regions harbor diverse and active populations of microorganisms. However, these microorganisms are subject to impacts of environmental perturbations. For example, climate change will modulate the distribution and activity of many cyanobacteria and algal species in polar environments that contribute significantly to global carbon fixation and oxygen production. Moreover, many microorganisms that have remained frozen for thousands of years can revive their metabolic activity and re-join the modern microbial community. For survival in freezing environments, polar microorganisms have established specific regulatory mechanisms which are now being challenged by new, rapidly changing environmental conditions. Remarkable progress has been made to uncover microbial adaptation to anthropogenic activities such as high irradiance, nutritional deprivation, UV-B radiation, heat, cold, desiccation, and heavy metals. Studies have enabled a basic understanding of gene regulatory pathways for morphological, physiological, metabolic, and genetic adaptations to various environmental stresses. To further elucidate physiological adaptation mechanisms and molecular diversity in polar regions, this Research Topic is focused on microbes in polar regions, looking at their biodiversity, ecological adaptations, the impact of climate change on their lifestyles, and biotechnological application of microbes for a sustainable future.
Author: Young Je Yoo
Publisher: Springer
ISBN: 9402410260
Category : Technology & Engineering
Languages : en
Pages : 208
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Book Description
This book provides a comprehensive introduction to all aspects of enzyme engineering, from fundamental principles through to the state-of-the-art in research and industrial applications. It begins with a brief history, describing the milestones of advancement in enzyme science and technology, before going on to cover the fundamentals of enzyme chemistry, the biosynthesis of enzymes and their production. Enzyme stability and the reaction kinetics during enzymatic reactions are presented to show how enzymes function during catalysis and the factors that affect their activity. Methods to improve enzyme performance are also presented, such as cofactor regeneration and enzyme immobilization. The book emphasizes and elaborates on the performance and characteristics of enzymes at the molecular level. Finally, the book presents recent advances in enzyme engineering and some key industrial application of enzymes addressing the present needs of society. This book presents essential information not only for undergraduate and graduate students, but also for researchers in academia and industry, providing a valuable reference for the development of commercial applications of enzyme technology.
Author: Pratima Bajpai
Publisher: Academic Press
ISBN: 0128010665
Category : Science
Languages : en
Pages : 121
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Book Description
Xylanolytic Enzymes describes the enzyme structure and its interaction with plant cell walls, the properties and production of different enzymes and their application, and the knowledge gathered on the hydrolysis mechanism of hemicellulose. The knowledge gathered about the hydrolysis mechanism of the hemicelluloses, especially xylans, has greatly promoted the rapid application of these enzymes in new areas. Recently there has been much industrial interest in xylan and its hydrolytic enzymatic complex, as a supplement and for the manufacturing of food, drinks, textiles, pulps and paper, and ethanol; and in xylitol production as a fermentation substrate for the production of enzymes. This book describes xylan as a major component of plant hemicelluloses. Presents a thorough overview of all aspects of xylanolytic enzymes Gives up-to-date authoritative information and cites pertinent research Includes studies on xylanase regulation and synergistic action between multiple forms of xylanase
Author: Vijai Kumar Gupta
Publisher: Springer
ISBN: 3319436791
Category : Technology & Engineering
Languages : en
Pages : 345
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Book Description
This volume summarizes our current knowledge on different biomass-converting enzymes and their potential use in converting biomass into simple sugar to generate bioenergy and other value added co-/by products. It consists of 13 chapters and is divided into three parts: cellulases; hemicellulases; and lignocellulose oxidoreductases. Written by international experts, the contributions offer clear and concise descriptions of both standard and new technologies. It is an invaluable reference resource for undergraduates, post-graduates, researchers and practitioners in the field of microbial enzymes for biofuel and biorefinery applications.
Author: Alane Beatriz Vermelho
Publisher: Bentham Science Publishers
ISBN: 1608053008
Category : Science
Languages : en
Pages : 334
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Book Description
Methods to Determine Enzymatic Activity is a textbook about industrial enzymes. The book features definitions, classifications and applications of selected enzymes important in industry and in biotechnological processes. Analytical methods for these enzymes are also included in the text. The main objective of this textbook is to provide readers information focused on the current analysis methods of enzymatic activity at qualitative and quantitative levels. Each chapter is about one specific enzyme and contains information about its substrate and some biochemical properties. The methodologies are presented as an experimental protocol allowing interested readers to reproduce the experimental methods detailed within the textbook. These protocols contain the principle of the technique, materials, methods, and all steps necessary for the determination of enzyme activity and interpretation of results. Each methodology is illustrated with photos and schemes for a better and clear understanding. This book, therefore, uniquely brings modern analysis techniques of industrial enzymes in a single easy to understand volume. This textbook is suitable for undergraduate enzymology courses and advanced industrial biotechnology and microbiology courses.
Author: W.M. Fogarty
Publisher: Springer Science & Business Media
ISBN: 9400907656
Category : Science
Languages : en
Pages : 482
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Book Description
Biotechnology is now one of the major growth areas in science and engineering and within this broad discipline enzyme technology is one of the areas earmarked for special and significant developments. This publication is the second edition of Microbial Enzymes and Biotechnol ogy which was originally published in 1983. In this edition the editors have attempted to bring together accounts (by the relevant experts) of the current status of the major areas of enzyme technology and specifically those areas of actual and/or potential commercial importance. Although the use of microbial enzymes may not have expanded at quite the rate expected a decade ago, there is nevertheless intense activity and considerable interest in the whole area of enzyme technology. Microbial enzymes have been used in industry for many centuries although it is only comparatively recently that detailed knowledge relating to their nature, properties and function has become more evident. Developments in the 1960s gave a major thrust to the use of microbial enzymes in industry. The commercial success of alkaline proteases and amyloglucosidases formed a bed-rock for subsequent research and development in the area.
Author: Michel Brienzo
Publisher: Springer Nature
ISBN: 9811636826
Category : Science
Languages : en
Pages : 508
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Book Description
This edited book provides knowledge about hemicelluloses biorefinery approaching production life cycle, circular economy, and valorization by obtaining value-added bioproducts and bioenergy. A special focus is dedicated to chemical and biochemical compounds produced from the hemicelluloses derivatives platform. Hemicelluloses are polysaccharides located into plant cell wall, with diverse chemical structures and properties. It is the second most spread organic polymer on nature and found in vast lignocellulosic materials from agro and industrial wastes, therefore, hemicelluloses are considered as abundant and renewable raw material/feedstock. Biorefinery concept contributes to hemicelluloses production associated with biomass industrial processes. Hemicelluloses are alternative sources of sugars for renewable fuels and as platform for chemicals production. This book reviews chemical processes for sugar production and degradation, obtaining of intermediate and final products, and challenges for pentose fermentation. Aspects of hemicelluloses chain chemical and enzymatic modifications are presented with focus on physicochemical properties improvement for bioplastic and biomaterial approaches. Hemicelluloses are presented as sources for advanced materials in biomedical and pharmaceutical uses, and as hydrogel for chemical and medicine deliveries. An interdisciplinary approach is needed to cover all the processes involving hemicelluloses, its conversion into final and intermediate value-added compounds, and bioenergy production. Covering this context, this book is of interest to teachers, students, researchers, and scientists dedicated to biomass valorization. This book is a knowledge source of basic aspects to advanced processing and application for graduate students, particularly. Besides, the book serves as additional reading material for undergraduate students (from different courses) with a deep interest in biomass and waste conversion, valorization, and chemical products from hemicelluloses
