Download or read book Computational Design and Mining for Enzyme Functions written by Wai Shun Mak and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Chapter 1: The ability to rationally engineer enzyme function has wide ranging applications and is a rigorous test on our understanding of enzyme function. We used a combination of genomic mining, structural biology, and machine-learning to determine the structural features that enable soluble aldehyde deformylating oxygenase (ADO) activity. These features were then used to introduce ADO activity into the small subunit of ribonucleotide reducatase. The ADO family of enzymes has previously only been observed in a small number of cyanobacteria but its ability to transform linear aldehydes into alkanes has significant implications in bioenergy, synthetic biology and chemoenzymatic synthesis applications. The enzymes discovered here from both genomic mining and engineering efforts yielded enzymes with novel specificity for medium chain aldehydes. In addition, they revealed that this functionality is observed in various species of Bacteria and Archaea and can be readily altered based on the structural features identified. Chapter 2:The ability to biosynthetically produce chemicals beyond what is commonly found in Nature requires the discovery of novel enzyme function. Here we utilize two approaches to discover enzymes that enable specific production of longer-chain (C5–C8) alcohols from sugar. The first approach combines bioinformatics and molecular modeling to mine sequence databases, resulting in a diverse panel of enzymes capable of catalyzing the targeted reaction. The median catalytic efficiency of the computationally selected enzymes is 75-fold greater than a panel of naively selected homologues. This integrative genomic mining approach establishes a unique avenue for enzyme function discovery in the rapidly expanding sequence databases. The second approach uses computational enzyme design to reprogram specificity. Each of these approaches results in enzymes with > 100-fold increase in specificity for the targeted reaction. When enzymes from either approach are integrated in vivo, longer-chain alcohol production increases over 10-fold and represents 95% of the total alcohol products. Chapter 3: Enzyme active sites have been through millions of years of evolution during which their active site microenvironments are fine-tuned. Active site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutate active site residues of L-threonine dehydrogenase from Thermoplasma volcanium and characterize the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues play an essential role in substrate recognition and catalysis, and that the native enzyme activity can be further enhanced roughly 6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs show that L-threonine dehydrogenase possesses promiscuous activities towards other chemically similar compounds previously not observed. Quantum mechanical calculations on these substrates’ hydride donating ability also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our quantitative analysis provides insights into connections between the details of enzyme active site structure and specific function. These results are directly applicable to rational enzyme design and engineering. Chapter 4: Keto acid decarboxylase (Kdc) is a key enzyme in producing keto acid derived higher alcohols, like isobutanol. The most active Kdc’s are found in mesophiles; the only reported Kdc activity in thermophiles is 2 orders of magnitude less active. Therefore, the thermostability of mesophilic Kdc limits isobutanol production temperature. Here, we report development of a thermostable 2-ketoisovalerate decarboxylase (Kivd) with 10.5-fold increased residual activity after 1h preincubation at 60 °C. Starting with mesophilic Lactococcus lactis Kivd, a library was generated using random mutagenesis and approximately 8,000 independent variants were screened. The top single-mutation variants were recombined. To further improve thermostability, 16 designs built using Rosetta Comparative Modeling were screened and the most active was recombined to form our best variant, LLM4. Compared to wild-type Kivd, a 13 °C increase in melting temperature and over 4-fold increase in half-life at 60 °C were observed. LLM4 will be useful for keto acid derived alcohol production in lignocellulytic thermophiles.
Download or read book New Enzymatic Functions Through Computational Design written by Gert Kiss and published by . This book was released on 2012 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Therapeutic Enzymes Function and Clinical Implications written by Nikolaos Labrou and published by Springer Nature. This book was released on 2019-09-03 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: Therapeutic enzymes exhibit fascinating features and opportunities, and represent a significant and promising subcategory of modern biopharmaceuticals for the treatment of several severe diseases. Research and drug developments efforts and the advancements in biotechnology over the past twenty years have greatly assisted the introduction of efficient and safe enzyme-based therapies for a range of both rare and common disorders. The introduction and regulatory approval of twenty different recombinant enzymes has enabled effective enzyme-replacement therapy. This volume aims to overview these therapeutic enzymes, focusing in particular on more recently approved enzymes produced by recombinant DNA technology. This volume is composed of four sections. Section 1 provides an overview of the production process and biochemical characterization of therapeutic enzymes, while Section 2 focuses upon the engineering strategies and delivery methods of therapeutic enzymes. Section 3 highlights the clinical applications of approved therapeutic enzymes, including aspects on their structure, indications and mechanisms of action. Together with information on these mechanisms, safety and immunogenicity issues and various adverse events of the recombinant enzymes used for therapy are discussed. Section 4, provides discussion on the prospective and future developments of new therapeutic enzymes. This book is aimed at academics, researchers and students undertaking advanced undergraduate/postgraduate programs in the biopharmaceutical/biotechnology area who wish to gain a comprehensive understanding of enzyme-based therapeutic molecules.
Download or read book Protein Engineering written by Huimin Zhao and published by John Wiley & Sons. This book was released on 2021-08-23 with total page 41 pages. Available in PDF, EPUB and Kindle. Book excerpt: A one-stop reference that reviews protein design strategies to applications in industrial and medical biotechnology Protein Engineering: Tools and Applications is a comprehensive resource that offers a systematic and comprehensive review of the most recent advances in the field, and contains detailed information on the methodologies and strategies behind these approaches. The authors—noted experts on the topic—explore the distinctive advantages and disadvantages of the presented methodologies and strategies in a targeted and focused manner that allows for the adaptation and implementation of the strategies for new applications. The book contains information on the directed evolution, rational design, and semi-rational design of proteins and offers a review of the most recent applications in industrial and medical biotechnology. This important book: Covers technologies and methodologies used in protein engineering Includes the strategies behind the approaches, designed to help with the adaptation and implementation of these strategies for new applications Offers a comprehensive and thorough treatment of protein engineering from primary strategies to applications in industrial and medical biotechnology Presents cutting edge advances in the continuously evolving field of protein engineering Written for students and professionals of bioengineering, biotechnology, biochemistry, Protein Engineering: Tools and Applications offers an essential resource to the design strategies in protein engineering and reviews recent applications.
Download or read book Computational Methods for Modeling Enzymes written by Steven James Bertolani and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzymes play a crucial role in modern biotechnology, industry, food processing and medical applications. Since their first discovered industrial use, man has attempted to discover new enzymes from Nature to catalyze different chemical reactions. In modern times, with the advent of computational methods, protein structure solutions, protein sequencing and DNA synthesis methods, we now have the tools to enable new approaches to rational enzyme engineering. With an enzyme structure in hand, a researcher may run an in silico experiment to sample different amino acids in the active site in order to identify new combinations which likely stabilize a transition-state-enzyme model. A suggested mutation can then be encoded into the desired enzyme gene, ordered, synthesized and tested. Although this truly astonishing feat of engineering and modern biotechnology allows the redesign of existing enzymes to acquire a new substrate specificity, it still requires a large amount of time, capital and technical capabilities. Concurrently, while making strides in computational protein design, the cost of sequencing DNA plummeted after the turn of the century. With the reduced cost of sequencing, the number of sequences in public databases of naturally occurring proteins has grown exponentially. This new, large source of information can be utilized to enable rational enzyme design, as long as it can be coupled with accurate modeling of the protein sequences. This work first describes a novel approach to reengineering enzymes (Genome Enzyme Orthologue Mining; GEO) that utilizes the vast amount of protein sequences in modern databases along with extensive computation modeling and achieves comparable results to the state-of-the-art rational enzyme design methods. Then, inspired by the success of this new method and aware of it's reliance on the accuracy of the protein models, we created a computational benchmark to both measure the accuracy of our models as well as improve it by encoding additional information about the structure, derived from mechanistic studies (Catalytic Geometry constraints; CG). Lastly, we use the improved accuracy method to automatically model hundreds of putative enzymes sequences and dock substrates into them to extract important features that are then used to inform experiments and design. This is used to reengineer a ribonucleotide reductase to catalyze a aldehyde deformylating oxygenase reaction.These chapters advance the field of rational enzyme engineering, by providing a novel technique that may enable efficient routes to rationally design enzymes for reactions of interest. These chapters also advance the field of homology modeling, in the specific domain in which the researcher is modeling an enzyme with a known chemical reaction. Lastly, these chapters and techniques lead to an example which utilizes highly accurate computational models to create features which can help guide the rational design of enzyme catalysts.
Download or read book Metabolic Pathway Design written by Pablo Carbonell and published by Springer Nature. This book was released on 2019-11-05 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook presents solid tools for in silico engineering biology, offering students a step-by-step guide to mastering the smart design of metabolic pathways. The first part explains the Design-Build-Test-Learn-cycle engineering approach to biology, discussing the basic tools to model biological and chemistry-based systems. Using these basic tools, the second part focuses on various computational protocols for metabolic pathway design, from enzyme selection to pathway discovery and enumeration. In the context of industrial biotechnology, the final part helps readers understand the challenges of scaling up and optimisation. By working with the free programming language Scientific Python, this book provides easily accessible tools for studying and learning the principles of modern in silico metabolic pathway design. Intended for advanced undergraduates and master’s students in biotechnology, biomedical engineering, bioinformatics and systems biology students, the introductory sections make it also useful for beginners wanting to learn the basics of scientific coding and find real-world, hands-on examples.
Download or read book Mining Designing Mechanisms and Applications of Extremophilic Enzymes written by Junpei Zhou and published by Frontiers Media SA. This book was released on 2021-12-29 with total page 199 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Approaches to Enzyme Structure and Function written by Harel Weinstein and published by S Karger Ag. This book was released on 1986 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Heterogeneous Catalysts written by Wey Yang Teoh and published by John Wiley & Sons. This book was released on 2021-02-23 with total page 768 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents state-of-the-art knowledge of heterogeneous catalysts including new applications in energy and environmental fields This book focuses on emerging techniques in heterogeneous catalysis, from new methodology for catalysts design and synthesis, surface studies and operando spectroscopies, ab initio techniques, to critical catalytic systems as relevant to energy and the environment. It provides the vision of addressing the foreseeable knowledge gap unfilled by classical knowledge in the field. Heterogeneous Catalysts: Advanced Design, Characterization and Applications begins with an overview on the evolution in catalysts synthesis and introduces readers to facets engineering on catalysts; electrochemical synthesis of nanostructured catalytic thin films; and bandgap engineering of semiconductor photocatalysts. Next, it examines how we are gaining a more precise understanding of catalytic events and materials under working conditions. It covers bridging pressure gap in surface catalytic studies; tomography in catalysts design; and resolving catalyst performance at nanoscale via fluorescence microscopy. Quantum approaches to predicting molecular reactions on catalytic surfaces follows that, along with chapters on Density Functional Theory in heterogeneous catalysis; first principles simulation of electrified interfaces in electrochemistry; and high-throughput computational design of novel catalytic materials. The book also discusses embracing the energy and environmental challenges of the 21st century through heterogeneous catalysis and much more. Presents recent developments in heterogeneous catalysis with emphasis on new fundamentals and emerging techniques Offers a comprehensive look at the important aspects of heterogeneous catalysis Provides an applications-oriented, bottoms-up approach to a high-interest subject that plays a vital role in industry and is widely applied in areas related to energy and environment Heterogeneous Catalysts: Advanced Design, Characterization and Applications is an important book for catalytic chemists, materials scientists, surface chemists, physical chemists, inorganic chemists, chemical engineers, and other professionals working in the chemical industry.
Download or read book Industrialization of Biology written by National Research Council and published by National Academies Press. This book was released on 2015-06-29 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt: The tremendous progress in biology over the last half century - from Watson and Crick's elucidation of the structure of DNA to today's astonishing, rapid progress in the field of synthetic biology - has positioned us for significant innovation in chemical production. New bio-based chemicals, improved public health through improved drugs and diagnostics, and biofuels that reduce our dependency on oil are all results of research and innovation in the biological sciences. In the past decade, we have witnessed major advances made possible by biotechnology in areas such as rapid, low-cost DNA sequencing, metabolic engineering, and high-throughput screening. The manufacturing of chemicals using biological synthesis and engineering could expand even faster. A proactive strategy - implemented through the development of a technical roadmap similar to those that enabled sustained growth in the semiconductor industry and our explorations of space - is needed if we are to realize the widespread benefits of accelerating the industrialization of biology. Industrialization of Biology presents such a roadmap to achieve key technical milestones for chemical manufacturing through biological routes. This report examines the technical, economic, and societal factors that limit the adoption of bioprocessing in the chemical industry today and which, if surmounted, would markedly accelerate the advanced manufacturing of chemicals via industrial biotechnology. Working at the interface of synthetic chemistry, metabolic engineering, molecular biology, and synthetic biology, Industrialization of Biology identifies key technical goals for next-generation chemical manufacturing, then identifies the gaps in knowledge, tools, techniques, and systems required to meet those goals, and targets and timelines for achieving them. This report also considers the skills necessary to accomplish the roadmap goals, and what training opportunities are required to produce the cadre of skilled scientists and engineers needed.
Download or read book Cell free Production written by Yuan Lu and published by Springer Nature. This book was released on 2023-10-18 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews the development of cell-free production platforms and offers an authoritative perspective of the latest advances and methodologies in cell-free production systems. Readers will discover the biomanufacturing potential of in vitro biotransformation (ivBT) employing purified cascade multi-enzymes, the development of hydrogel-based multi-enzymatic systems for biosynthesis, and novel insights into the optimization of biocatalytic processes. Additionally, the book explores the cell-free production and regeneration of cofactors, shedding light on strategies to enhance the efficiency and sustainability of cellular processes. In this book, particular attention is given to the progress of cell-free in vitro evolution techniques for optimizing enzyme performance, and the book also presents the integration of rapid and finely-tuned expression systems for deployable sensing applications, revolutionizing the field of biosensing. The synthesis and electrophysiological analysis of multipass voltage-gated ion channels tethered in microsomal membranes are explored, providing a deep understanding of cellular function at the molecular level. Lastly, the book covers compartmentalized cell-free expression systems for building synthetic cells, showcasing the potential for constructing artificial cellular systems with unique functionalities. Given its breadth, this book appeals to academics, researchers, and professionals interested in the forefront of biotechnology, and together with the companion volume “Cell-free Macromolecular Synthesis”, both books highlight the research progresses on the basic and applied research of cell-free production systems in the last few years, being invaluable resources in the field. Chapter “Cell-free synthesis and electrophysiological analysis of multipass voltage-gated ion channels tethered in microsomal membranes” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Download or read book Biocatalysts and Enzyme Technology written by Klaus Buchholz and published by John Wiley & Sons. This book was released on 2012-12-21 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition of a bestselling textbook offers an instructive and comprehensive overview of our current knowledge of biocatalysis and enzyme technology. The book now contains about 40% more printed content. Three chapters are completely new, while the others have been thoroughly updated, and a section with problems and solutions as well as new case studies have been added. Following an introduction to the history of enzyme applications, the text goes on to cover in depth enzyme mechanisms and kinetics, production, recovery, characterization and design by protein engineering. The authors treat a broad range of applications of soluble and immobilized biocatalysts, including wholecell systems, the use of non-aqueous reaction systems, applications in organic synthesis, bioreactor design and reaction engineering. Methods to estimate the sustainability, important internet resources and their evaluation, and legislation concerning the use of biocatalysts are also covered.
Download or read book Enzyme Cascade Design and Modelling written by Selin Kara and published by Springer Nature. This book was released on 2021-02-24 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of the recent developments achieved in the field of chemo/enzymatic cascades with topics spanning from design (in vitro and in vivo) to kinetic- and process modelling as well as process control. Opportunities and challenges of building multi-step chemo/enzymatic reactions are discussed, whereby the latter are critically assessed in each chapter and methods to ease the implementation are explored. Both, multi-enzymatic cascades and chemo-enzymatic cascades are presented with the motivation of combining the strengths of these two worlds (e.g. selectivity, activity and robustness) not neglecting the obstacles and challenges of such endeavour. Furthermore, the use of non-conventional media for catalytic cascade reactions, recent achievements and potential for future developments in a technical environment are addressed.
Download or read book Computational Science and Its Applications ICCSA 2008 written by Osvaldo Gervasi and published by Springer. This book was released on 2008-06-28 with total page 1297 pages. Available in PDF, EPUB and Kindle. Book excerpt: This two-volume set is assembled following the 2008 International Conference on Computational Science and Its Applications, ICCSA 2008, a premium int- national event held in Perugia, Italy, from June 30 to July 3, 2008. The collection of fully refereed high-quality original works accepted as theme papers for presentation at ICCSA 2008 are published in this LNCS proceedings set. This outstanding collection complements the volume of workshop papers, traditionally published by IEEE Computer Society. The continuous support of computational science researchers has helped ICCSA to become a ?rmly established forum in the area of scienti?c computing and the conference itself become a recurring scienti?c and professional meeting that cannot be given up. The computational science ?eld, based on fundamental disciplines such as mathematics, physics, and chemistry, is ?nding new computational approaches to foster the human progress in heterogeneous and fundamental areas such as aerospace and automotive industries, bioinformatics and nanotechnology studies, networks and grid computing, computational geometry and biometrics, computer education, virtual reality, and art. Due to the growing complexity of many ch- lenges in computational science, the use of sophisticated algorithms and eme- ing technologies is inevitable. Together, these far-reaching scienti?c areas help to shape this conference in the areas of state-of-the-art computational science research and applications, encompassing the facilitating theoretical foundations and the innovative applications of such results in other areas.
Download or read book Computational Design of Ligand Binding Proteins written by Barry L. Stoddard and published by Humana. This book was released on 2016-04-20 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a collection of protocols and approaches for the creation of novel ligand binding proteins, compiled and described by many of today's leaders in the field of protein engineering. Chapters focus on modeling protein ligand binding sites, accurate modeling of protein-ligand conformational sampling, scoring of individual docked solutions, structure-based design program such as ROSETTA, protein engineering, and additional methodological approaches. Examples of applications include the design of metal-binding proteins and light-induced ligand binding proteins, the creation of binding proteins that also display catalytic activity, and the binding of larger peptide, protein, DNA and RNA ligands. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Download or read book Marine Enzymes for Biocatalysis written by Antonio Trincone and published by Elsevier. This book was released on 2013-09-30 with total page 576 pages. Available in PDF, EPUB and Kindle. Book excerpt: Marine bioprospecting is a highly topical subject - in both applied and basic research - but, as yet, the marine ecosystem is a relatively unexplored source of natural bioactive substances with potential therapeutic activity. This book addresses the use of marine enzymes in biocatalysis through a series of chapters from leading scientists within academic and industrial fields. Biocatalytic processes can take advantage of the habitat-related properties of marine enzymes, such as salt tolerance, hyperthermostability, barophilicity, cold adaptivity, and so on, whilst also taking into consideration substrate specificity and affinity. These evolved properties are linked to the metabolic functions of the enzymes and to the ecological aspects of the natural source. New properties can also be discovered at the molecular level of catalysis, particularly concerning the stereochemical characteristics of products.Marine enzymes for biocatalysis initially examines the nature and level of interest in marine biological diversity, and outlines the fundamentals of biocatalysis. It goes on to detail sources of marine enzymes, and to analyse examples from both chemical and stereochemical viewpoints of catalysis, including microbial enzymes and animal or plant sources. The book goes on to explore the future potential of marine bioprospecting in biocatalysis. - Compiles studies from leading scientists in a direct and accessible format. Includes practical descriptions of results, adding further details not often covered in formal articles - Takes a molecular view which fully explains the enzymatic aspects of reactions, particularly regarding biocatalytic characteristics and descriptions of bioprocesses - Selects examples of chemical and stereochemical aspects of enzymatic action with respect to known terrestrial counterparts
Download or read book Computational Structural Biology written by Torsten Schwede and published by World Scientific. This book was released on 2008 with total page 790 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a comprehensive introduction to Landau-Lifshitz equations and Landau-Lifshitz-Maxwell equations, beginning with the work by Yulin Zhou and Boling Guo in the early 1980s and including most of the work done by this Chinese group led by Zhou and Guo since. The book focuses on aspects such as the existence of weak solutions in multi dimensions, existence and uniqueness of smooth solutions in one dimension, relations with harmonic map heat flows, partial regularity and long time behaviors. The book is a valuable reference book for those who are interested in partial differential equations, geometric analysis and mathematical physics. It may also be used as an advanced textbook by graduate students in these fields.
