Download or read book Non Ribosomal Peptide Biosynthesis and Engineering written by Michael Burkart and published by Springer Nature. This book was released on 2023-05-15 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides new technologies on NRPSs and related carrier protein dependent synthases, including polyketide synthases (PKS) and fatty acid synthases (FAS). Chapters detail enzymology, structural biology, proteopromics, chemical biology, natural product chemistry, and bioinformatics. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Non-Ribosomal Peptide Biosynthesis and Engineering: Methods and Protocols aims to feature methods that will be beneficial to new researchers, and those wanting to adopt new methodologies into their research.
Download or read book Engineering Nonribosomal Peptide Synthesis by Directed Evolution and Module Reassembly written by Philipp Stephan and published by . This book was released on 2024* with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the last decades, discovery rates of new antibiotics have declined while the occurrence of multi-resistant pathogens has increased, leading towards a post-antibiotic era. Many current antibiotics are natural products or derivatives, known for their excellent bioactivities but complex structures that complicate synthetic production. Many antibiotics, like penicillin and vancomycin, are peptides produced by nonribosomal peptide synthetases (NRPS). These multi-modular enzyme complexes function like assembly lines, with each module adding a specific amino acid to the peptide through the biocatalytic activities of distinct domains. Targeted NRPS engineering to alter structures of the produced peptides has faced challenges, but directed evolution of NRPS domains seems to offer a promising solution. This thesis presents a straightforward method for the directed evolution of adenylation (A) domains using LC-MS/MS detection of dipeptides in cell lysates, demonstrating its power by engineering the GrsB1 A domain from gramicidin S biosynthesis to select for L-piperazic acid (Piz) instead of its native substrate L-Pro without reducing enzyme activity. The modified antibiotic, Piz-gramicidin S, showed improved bioactivity. Despite compatibility issues between NRPS domains, kinetic analyses revealed that A domain substrate preferences ultimately determine final product ratios. Additionally, the thesis proposes a novel DNA-based approach for NRPS engineering, using zinc finger domains that bind specific DNA sequences to simplify module rearrangement by making NRPSs DNA-templated. This method offers a more efficient alternative to traditional cloning techniques by replacing the handling of large NRPS genes with much shorter sequences of the zinc finger domains. Overall, this research advances the engineering of NRPSs for developing new antibiotics with better efficacy against resistant pathogens and highlights the usefulness of directed evolution in this context.
Download or read book Expanding the Toolbox for Engineering Nonribosomal Peptide Synthetases written by Farzaneh Pourmasoumi and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nonribosomal peptide synthetases (NRPSs) are an important source of pharmaceutically valuable natural products, including antibiotics. In depth understanding of enzymatic interactions responsible for the biosynthesis of these compounds by NRPSs is essential for re-engineering of these proteins to create structural diversity. In this work, we establish tools that expand the understanding and engineering of nonribosomal peptide synthetases.
Download or read book Engineering of a Novel Nonribosomal Peptide Synthetase for Alanyl glutamine Production written by Jennifer Fick Brannock and published by . This book was released on 2006 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Nonribosomal Peptide Synthetases Engineering Characterization and Biotechnological Potential written by Reto Daniel Zwahlen and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Engineering and Characterisation of Non ribosomal Peptide Synthetases written by Andreas Tietze and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Chemical and Biological Synthesis written by Nick J Westwood and published by Royal Society of Chemistry. This book was released on 2018-08-16 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic chemistry plays a central role in many areas of chemical biology; utilising recent case studies, the goal of Chemical and Biological Synthesis is to highlight the full impact that the preparation of novel reagents can have in chemical biology. Covering the synthetic approaches that can be applied across the whole field of chemical biology, this book provides synthetic chemists with the broader context to which their work contributes and the biological questions that can be addressed through it. An ideal guide for postgraduate students and researchers in synthetic organic chemistry and chemical biology, Chemical and Biological Synthesis introduces synthetic techniques and methods to those who wish to incorporate synthesis for the first time in their biology-focused research programmes.
Download or read book Lasso Peptides written by Yanyan Li and published by Springer. This book was released on 2014-10-21 with total page 113 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lasso peptides form a growing family of fascinating ribosomally-synthesized and post-translationally modified peptides produced by bacteria. They contain 15 to 24 residues and share a unique interlocked topology that involves an N-terminal 7 to 9-residue macrolactam ring where the C-terminal tail is threaded and irreversibly trapped. The ring results from the condensation of the N-terminal amino group with a side-chain carboxylate of a glutamate at position 8 or 9, or an aspartate at position 7, 8 or 9. The trapping of the tail involves bulky amino acids located in the tail below and above the ring and/or disulfide bridges connecting the ring and the tail. Lasso peptides are subdivided into three subtypes depending on the absence (class II) or presence of one (class III) or two (class I) disulfide bridges. The lasso topology results in highly compact structures that give to lasso peptides an extraordinary stability towards both protease degradation and denaturing conditions. Lasso peptides are generally receptor antagonists, enzyme inhibitors and/or antibacterial or antiviral (anti-HIV) agents. The lasso scaffold and the associated biological activities shown by lasso peptides on different key targets make them promising molecules with high therapeutic potential. Their application in drug design has been exemplified by the development of an integrin antagonist based on a lasso peptide scaffold. The biosynthesis machinery of lasso peptides is therefore of high biotechnological interest, especially since such highly compact and stable structures have to date revealed inaccessible by peptide synthesis. Lasso peptides are produced from a linear precursor LasA, which undergoes a maturation process involving several steps, in particular cleavage of the leader peptide and cyclization. The post-translational modifications are ensured by a dedicated enzymatic machinery, which is composed of an ATP-dependent cysteine protease (LasB) and a lactam synthetase (LasC) that form an enzymatic complex called lasso synthetase. Microcin J25, produced by Escherichia coli AY25, is the archetype of lasso peptides and the most extensively studied. To date only around forty lasso peptides have been isolated, but genome mining approaches have revealed that they are widely distributed among Proteobacteria and Actinobacteria, particularly in Streptomyces, making available a rich resource of novel lasso peptides and enzyme machineries towards lasso topologies.
Download or read book Biocatalysis written by Peter Grunwald and published by Imperial College Press. This book was released on 2009 with total page 1052 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book covers the fundamentals of the field of biocatalysis that are not treated in such detail (or even not at all) in existing biocatalysis books or biochemistry textbooks. It of course does not substitute existing biochemistry textbooks but will serve a suitable supplement as it discusses biochemical fundamentals in connection with the respective topics.With focus on the interdisciplinary nature of biocatalysis, the book contains many aspects of fundamental organic chemistry and some of inorganic chemistry as well, which should make it interesting not only for biochemistry but also for chemistry students. An important theme being emphasized in the book is that applied biocatalysis is one of the main prerequisites for a sustainable development.The topics covered ranges from basic enzyme chemistry (biosynthesis, structure, properties, interaction forces, kinetics) to a detailed description of catalytic mechanisms. It covers the fundamentals of the different enzyme classes together with their applications in native and in immobilized state or in the form of whole cells in aqueous as well as non-conventional media. Topics such as catalytic antibodies, nucleic acid catalysts, non-ribosomal peptide synthesis, evolutionary methods, and the design of cells are also included.
Download or read book Non ribosomal Peptide Synthetase Engineering Focusing on the Condensation Domain and the Condensation adenylation Domain Interface written by Janik Kranz and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Natural Product Biosynthesis written by Christopher T. Walsh and published by Royal Society of Chemistry. This book was released on 2017-04-28 with total page 787 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook describes the types of natural products, the biosynthetic pathways that enable the production of these molecules, and an update on the discovery of novel products in the post-genomic era.
Download or read book Two Approaches to Dissecting the Role of the MbtH like Protein in Nonribosomal Peptide Synthesis written by Rebecca Schomer and published by . This book was released on 2018 with total page 140 pages. Available in PDF, EPUB and Kindle. Book excerpt: Natural products (NPs) are an important source for antibacterial, antifungal and anticancer drugs. One medically relevant class of NP, nonribosomal peptides (NRPs), are constructed by a conserved enzymology called nonribosomal peptide synthetases (NRPSs). Efforts to metabolically engineer next generation antibacterial NRPs has been slow due to an incomplete understanding of NRPS enzymology. The recent discovery that MbtH-like proteins (MLPs), a superfamily of short polypeptides with chaperone-like properties, are required for the solubility and activity of many NRPSs was a significant breakthrough in our ability to characterize NRPSs in vitro. While MLP-encoding genes are usually found within the NRPS-encoding gene cluster they influence, cross pathway MLP/NRPS interactions occur when more than one MLP is encoded in a genome. These interactions are complex and have been shown to be variable between both noncognate and cognate MLP/NRPS partners. Prior to this thesis, we did not have a detailed understanding of which aspects of the MLP are required for functional interaction with an NRPS. Using Enterobactin (ENT) biosynthesis from Escherichia coli as a model system, this thesis makes progress characterizing the role of the MbtH-like protein (MLP) in NRPS enzymology by dissecting MLP/NRPS interactions by two approaches. First, I probe the ability of noncognate MLPs to interact in vivo and in vitro with the MLP-dependent NRPS, EntF. Second, I target the cognate MLP, YbdZ, and perform a complete survey of the MLP residues involved in functional interactions with EntF. These analyses of this model MLP/NRPS pair is the most detailed to date and offers valuable insight into future directed evolution studies of MLPs and MLP-dependent NRPSs. Significantly, this work demonstrates the complexities of MLP/NRPS interactions and highlights challenges that must be addressed when engineering MLP-dependent NRPS.
Download or read book Systems Metabolic Engineering written by Christoph Wittmann and published by Springer Science & Business Media. This book was released on 2012-06-15 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Metabolic Engineering is changing the way microbial cell factories are designed and optimized for industrial production. Integrating systems biology and biotechnology with new concepts from synthetic biology enables the global analysis and engineering of microorganisms and bioprocesses at super efficiency and versatility otherwise not accessible. Without doubt, systems metabolic engineering is a major driver towards bio-based production of chemicals, materials and fuels from renewables and thus one of the core technologies of global green growth. In this book, Christoph Wittmann and Sang-Yup Lee have assembled the world leaders on systems metabolic engineering and cover the full story – from genomes and networks via discovery and design to industrial implementation practises. This book is a comprehensive resource for students and researchers from academia and industry interested in systems metabolic engineering. It provides us with the fundaments to targeted engineering of microbial cells for sustainable bio-production and stimulates those who are interested to enter this exiting research field.
Download or read book Activity Based Protein Profiling written by Benjamin F. Cravatt and published by Springer. This book was released on 2019-01-25 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a collection of contemporary perspectives on using activity-based protein profiling (ABPP) for biological discoveries in protein science, microbiology, and immunology. A common theme throughout is the special utility of ABPP to interrogate protein function and small-molecule interactions on a global scale in native biological systems. Each chapter showcases distinct advantages of ABPP applied to diverse protein classes and biological systems. As such, the book offers readers valuable insights into the basic principles of ABPP technology and how to apply this approach to biological questions ranging from the study of post-translational modifications to targeting bacterial effectors in host-pathogen interactions.
Download or read book Dissecting Natural Product Biosynthetic Enzymes Using Siderophore Systems written by Vladimir Vinnik and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nonribosomal peptides (NRPs) and polyketides are medically and industrially vital natural products of diverse biological function, including many of the most commonly used antibiotics. These natural products are biosynthesized by nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), respectively. The rising threat of antibiotic drug resistance is further exacerbated by the dramatic downturn in conventional drug discovery efforts. Combinatorial biosynthesis of NRPSs and PKSs is a promising approach for producing new antibiotics and other pharmaceuticals by engineering these biosynthetic enzymes. This thesis examines the use of NRPS and PKS-produced siderophores to study natural product biosynthesis through directed evolution approaches. In particular, the substrate specificity of the adenylation (A) domain of the NRPS EntF, from enterobactin biosynthesis in E. coli, is investigated using multi-site saturation mutagenesis of the substrate binding pocket. This work provided key insights into how the gatekeeper A domains recognize their substrates. Additionally, the structures of two new hybrid NRPS/PKS-produced siderophore analogs, fabrubactin (FBN) A and B, made by Agbrobacterium fabrum strain C58, were solved and the core biosynthetic enzymes were characterized. Determining the structures of FBN A and B allows for the use of directed evolution approaches to study aspects of the NRPS and PKS enzymology involved in the formation of these siderophores. Additionally, our data revealed the presence of unique structural moieties suggesting the involvement of unusual enzymology. The fundamentals learned from these directed evolution approaches can be applied to engineering enzymes involved in the biosynthesis of molecules that are important for medicine, industry, and agriculture.
Download or read book Introduction to Peptide Science written by Ian W. Hamley and published by John Wiley & Sons. This book was released on 2020-06-08 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides an interdisciplinary introduction to peptide science, covering their properties and synthesis, as well as many contemporary applications Peptides are biomolecules comprised of amino acids which play an important role in modulating many physiological processes in our body. This book presents an interdisciplinary approach and general introduction to peptide science, covering contemporary topics including their applicability in therapeutics, peptide hormones, amyloid structures, self-assembled structures, hydrogels, and peptide conjugates including lipopeptides and polymer-peptide conjugates. In addition, it discusses basic properties and synthesis clearly and concisely. Taking a logical approach to the subject, Introduction to Peptide Science gives readers the fundamental knowledge that is required to understand the cutting-edge material which comes later in the book. It offers readers in-depth chapter coverage of the basic properties of peptides; synthesis; amyloid and peptide aggregate structures; antimicrobial peptides and cell-penetrating peptides; and peptide therapeutics and peptide hormones. Introduces readers to peptide science, including synthesis and properties Provides unique content covering properties, synthesis, self-assembly, aggregation, and applications Summarizes contemporary topics in an accessible fashion including applications in therapeutics, peptide hormones, amyloid structures, self-assembled structures, hydrogels, and peptide conjugates including lipopeptides Presented at an introductory level for the benefit of students and researchers who are new to the subject Introduction to Peptide Science is an ideal text for undergraduate students of chemistry, biochemistry, and other related biological subjects, and will be a valuable resource for postgraduate students and researchers involved in peptide science and its applications.
Download or read book Complex Peptide Natural Products Biosynthetic Principles Challenges and Opportunities for Pathway Engineering written by Sebastian Leonhard Wenski and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
