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Expansion Of The Genetic Code Unnatural Amino Acids And Their Applications
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Book Synopsis Expansion of the Genetic Code: Unnatural Amino Acids and Their Applications by : Subhendu Sekhar Bag
Download or read book Expansion of the Genetic Code: Unnatural Amino Acids and Their Applications written by Subhendu Sekhar Bag and published by Frontiers Media SA. This book was released on 2022-08-26 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Non-Natural Amino Acids written by and published by Academic Press. This book was released on 2009-07-24 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: By combining the tools of organic chemistry with those of physical biochemistry and cell biology, Non-Natural Amino Acids aims to provide fundamental insights into how proteins work within the context of complex biological systems of biomedical interest. The critically acclaimed laboratory standard for 40 years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. With more than 400 volumes published, each Methods in Enzymology volume presents material that is relevant in today's labs -- truly an essential publication for researchers in all fields of life sciences. Demonstrates how the tools and principles of chemistry combined with the molecules and processes of living cells can be combined to create molecules with new properties and functions found neither in nature nor in the test tube Presents new insights into the molecular mechanisms of complex biological and chemical systems that can be gained by studying the structure and function of non-natural molecules Provides a "one-stop shop" for tried and tested essential techniques, eliminating the need to wade through untested or unreliable methods
Book Synopsis Directed Evolution of and with Expanded Genetic Codes by : Chang C. Liu
Download or read book Directed Evolution of and with Expanded Genetic Codes written by Chang C. Liu and published by . This book was released on 2009 with total page 438 pages. Available in PDF, EPUB and Kindle. Book excerpt: By expanding the genetic code to allow the cotranslational incorporation of unnatural amino acids, one can site-specifically introduce unique chemical functionality into proteins in vivo. By using such expanded genetic codes in directed evolution, one can impose selection for novel protein function wherein variants containing unnatural amino acids will be selected should the unnatural amino acids confer a functional advantage. I first describe the expansion of E. coli 's genetic code for the site-specific incorporation of the unnatural amino acid sulfotyrosine and the subsequent use of this expanded genetic code for the expression and study of several proteins including sulfo-hirudin and sulfated anti-HIV antibodies. I then describe the development of a phage-based system for evolution with expanded genetic codes and the application of this system for directed evolution, through which proteins that use unnatural amino acids for enhanced function can emerge from selection. This work demonstrates the value of genetically encoding more than the 20 natural amino acids for protein engineering applications and shows that these expanded genetic codes can confer a selective advantage.
Book Synopsis Applications of an Expanded Genetic Code by : Eric M. Brustad
Download or read book Applications of an Expanded Genetic Code written by Eric M. Brustad and published by ProQuest. This book was released on 2008 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: With an ever expanding genetic code it is no longer a question of whether an unnatural amino acid can be introduced into a protein sequence, but what can be done with them. This thesis describes the introduction of novel amino acids to the genetic codes of E. coli and yeast and the applications of those amino acids towards novel protein biochemistry and the study of biomolecular structure and function. This includes the development of orthogonal protein labeling strategies that allow the site-specific attachment of biophysical probes and other molecules onto a protein surface. An unnatural ketone containing amino acid is described that allows the general and efficient introduction of fluorophores and spin probes onto a protein surface. This chemistry is exploited for the site-specific double labeling of proteins with fluorophores and the utility of this methodology is demonstrated by the examination of bacteriophage T4 lysozyme folding via single molecule fluorescence energy transfer. To expand the orthogonal chemistry presented by unnatural amino acid mutagenesis, the addition of a boronic acid containing amino acid to the genetic code of E. coli is also described. The unique chemistry of this functionality is exploited for the site-specific labeling of proteins with fluorophores through Suzuki coupling reactions as well as the formation boronic esters with diol containing compounds. This latter chemistry is also useful for the genetic encoding of carbohydrate recognition into a protein sequence as well as the development of a single step scarless protein purification methodology. The evolution of the E. coli leucyl tRNA synthetase for the site-selective introduction of methionine, cysteine and alanine analogs into proteins in yeast is also described. From this work, a single tRNA synthetase that shows promiscuous activity for over ten unnatural amino acid structures is investigated. Finally, a project investigating the role and source of reactive oxygen species in cytokine signaling is also be briefly discussed.
Book Synopsis Genetic Code Expansion in Biochemical Investigations and Biomedical Applications by : Nanxi Wang
Download or read book Genetic Code Expansion in Biochemical Investigations and Biomedical Applications written by Nanxi Wang and published by . This book was released on 2017 with total page 165 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic code expansion provides a powerful tool for site-specific incorporation of unnatural amino acids (unAAs) with novel biochemical and physiological properties into proteins in live cells and organisms. To achieve this, a nonsense codon suppression system, which consists of an orthogonal aminoacyl-tRNA synthetase (aaRS) and tRNA pair that specifically decodes a nonsense codon (e.g., amber codon and quadruplet codon) with an unAA but do not "cross talk" with their endogenous counterparts, was established. This Ph.D. thesis presents our efforts on evolution and application of nonsense codon suppression systems for biochemical and biomedical investigations.
Book Synopsis Engineering the Genetic Code by : Nediljko Budisa
Download or read book Engineering the Genetic Code written by Nediljko Budisa and published by John Wiley & Sons. This book was released on 2006-05-12 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to introduce non-canonical amino acids in vivo has greatly expanded the repertoire of accessible proteins for basic research and biotechnological application. Here, the different methods and strategies to incorporate new or modified amino acids are explained in detail, including a lot of practical advice for first-time users of this powerful technique. Novel applications in protein biochemistry, genomics, biotechnology and biomedicine made possible by the expansion of the genetic code are discussed and numerous examples are given. Essential reading for all molecular life scientists who want to stay ahead in their research.
Book Synopsis Genetically Incorporated Non-Canonical Amino Acids by : Yu-Hsuan Tsai
Download or read book Genetically Incorporated Non-Canonical Amino Acids written by Yu-Hsuan Tsai and published by Springer Nature. This book was released on 2023-06-05 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume explores non-canonical amino acids (ncAAs) through their site-specific incorporation by genetic code expansion (GCE). The collection provides a broad resource of methods for implementing GCE in E. coli, mammalian cells, and animals, highlighting specific applications ranging from fluorescence labeling to photocontrol and the study of protein post-translational modification. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Genetically Incorporated Non-Canonical Amino Acids: Methods and Protocols serves as an ideal source of methodologies that can be adapted and extended, migrated to different model systems, and combined in new ways to help explore a wide range of biological questions and to augment industrial and pharmaceutical protein engineering.
Book Synopsis Synthetic DNA and RNA Programming by : Patrick O’Donoghue
Download or read book Synthetic DNA and RNA Programming written by Patrick O’Donoghue and published by MDPI. This book was released on 2019-11-19 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dear Colleagues, Synthetic biology is a broad and emerging discipline that capitalizes on recent advances in molecular biology, genetics, protein and RNA engineering and omics technologies. These technologies have transformed our ability to reveal the biology of the cell and the molecular basis of disease. This Special Issue on “Synthetic RNA and DNA Programming” features original research articles and reviews, highlighting novel aspects of basic molecular biology and the molecular mechanisms of disease that were uncovered by the application and development of novel synthetic biology-driven approaches.
Book Synopsis Unnatural Amino Acid Incorporation for Genetic Code Expansion in Mammalian Cells by : Jeffrey Kunio Takimoto
Download or read book Unnatural Amino Acid Incorporation for Genetic Code Expansion in Mammalian Cells written by Jeffrey Kunio Takimoto and published by . This book was released on 2011 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt: The genetic code of most organisms was evolved to encode 20 amino acids. Although the ability to encode 20 amino acids provides the basis to translate proteins necessary for life, researchers are also limited to these 20 amino acids for conventional site-directed mutagenesis. The ability to encode unnatural amino acids provides researchers the ability to circumvent the limitation imposed by the genetic code. Genetically encoding unnatural amino acids provides researchers the means to not only mimic naturally occurring posttranslational modifications but also the ability to encode amino acids with new physical or chemical properties to study biological processes. The incorporation of unnatural amino acids into proteins had been developed in Escherichia coli and also in yeast. We have developed a methodology to genetically incorporate unnatural amino acids in mammalian cells in response to an amber codon (UAG). The incorporation of unnatural amino acids is high in E. coli and yeast, but the incorporation in mammalian cells is relatively low. In addition to developing the system to incorporate unnatural amino acids in mammalian cells, we have also improved suppression efficiencies by modifying the synthetase and unnatural amino acid. To incorporate unnatural amino acids in response to an amber codon, the tRNA anticodon is mutated from a GUA to a CUA. We were able to show that engineering the anticodon-binding domain of the synthetase could enhance the recognition of the tRNA and thus increased suppression efficiencies. Furthermore, by masking the carboxyl group of the amino acid by an ester group, we were able to increase the bioavailability of an unnatural amino acid to further increase suppression efficiencies. Most evolved synthetases aminoacylate unnatural amino acids that are structurally similar to the native substrate of the wild-type synthetase. We were able to adapt Methanosarcina mazei pyrrolysine synthetase (PylRS) to charge a considerable disparate amino acid from its native substrate, O-methyl-L-tyrosine. In addition, the X-ray crystal structure was solved for the evolved PylRS complexed with O-methyl-L-tyrosine at 1.75Å. This multifaceted approach provides the basis to engineer the PylRS to incorporate a significantly diverse selection of unnatural amino acids than previously anticipated.
Book Synopsis Protein Engineering by : Huimin Zhao
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.
Book Synopsis Genetic Incorporation of Unnatural Amino Acids and Its Applications by : Mingchao Kang
Download or read book Genetic Incorporation of Unnatural Amino Acids and Its Applications written by Mingchao Kang and published by . This book was released on 2013 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Unnatural Amino Acids in Proteins for Development of Novel Biochemical Tools by : Jordan Villa
Download or read book Unnatural Amino Acids in Proteins for Development of Novel Biochemical Tools written by Jordan Villa and published by . This book was released on 2015 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt: Unnatural amino acids (UAAs) permit the incorporation of novel biochemical functionalities into proteins. This expansion of the genetic code has enabled enhanced spatial and temporal control of protein activity and conferred novel protein reactivity. This study examines the incorporation of three UAAs: fluoro-tyrosine, ortho-nitrobenzyl-tyrosine, and propargyloxy-phenylalanine towards various applications. Each UAA was successfully incorporated into a protein of interest (GFP or PRMT1) to facilitate the desired manipulation of protein function. The resulting alterations to GFP fluorescence, PRMT1 activity, or immobilization using Glaser-Hay bioconjugation demonstrate the success and practicality of the utilization of UAAs in the development of novel biochemical tools.
Book Synopsis Noncanonical Amino Acids by : Edward A. Lemke
Download or read book Noncanonical Amino Acids written by Edward A. Lemke and published by . This book was released on 2018 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Utilization of Unatural Amino Acids to Modulate Protein Structure and Function by : John Halonski
Download or read book Utilization of Unatural Amino Acids to Modulate Protein Structure and Function written by John Halonski and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are capable of an astounding array of functions using only the 20 canonical amino acids; however, the ability to add new functional groups to the genetic code through the utilization of unnatural amino acids (UAAs) has greatly expanded our ability to study and manipulate proteins. By expanding the diversity of functional groups within proteins, a wide variety of applications in industry as well as in fields such as diagnostics, biochemistry, and materials science are now possible. These applications have further been expanded through the development and optimization of bioorthogonal reactions which can occur under physiological conditions with a high degree of specificity, allowing modulation of the structure and function of proteins within their natural state. Several applications of UAA technology involving bioorthogonal reactions will be explored in this thesis. Optimization of a previously developed bioorthogonal Glaser-Hay reaction between a protein and a fluorophore will be discussed. A further application of the Glaser-Hay reaction involving natural product synthesis will also be explored. The utilization of UAA technology to form trivalent conjugates containing multiple functionalities will be described. Furthermore, the development and optimization of organic reactions leading to the formation of trivalent structures will be explored with the intention of translating these reactions to biological systems. The ability to site-specifically immobilize a hyperthermophilic carboxylesterase enzyme onto a stabilizing resin will also be discussed and the benefits of protein immobilization will be demonstrated. Finally, the synthesis and development of novel TMS and aldehyde UAAs will be described and their applications will be explored. The applications highlighted in each chapter demonstrate some of the numerous possibilities that can be explored through modulation of the building blocks of proteins.
Book Synopsis Genetic Incorporation of Unnatural Amino Acids and Its Applications by : Hyun Soo Lee
Download or read book Genetic Incorporation of Unnatural Amino Acids and Its Applications written by Hyun Soo Lee and published by . This book was released on 2009 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt: To probe protein-DNA interactions, (2,2'-bipyridin-5-yl)alanine (Bpy-Ala) or p-benzoyl-L-phenylalanine ( pBpa) were incorporated into the E. coli catabolite activator protein (CAP). In the presence of Cu (II) and 3-mercaptopropionic acid, a CAP mutant containing Bpy-Ala cleaved double-stranded DNA with high sequence-specificity. The other CAP mutant containing pBpa formed a covalent complex with a DNA fragment containing the consensus operator sequence upon UV irradiation. These two experiments demonstrated that Bpy-Ala and p Bpa can be used to map the molecular details of protein-nucleic acid interactions.
Book Synopsis Unnatural Amino Acids by : Loredano Pollegioni
Download or read book Unnatural Amino Acids written by Loredano Pollegioni and published by Humana Press. This book was released on 2011-10-05 with total page 409 pages. Available in PDF, EPUB and Kindle. Book excerpt: Even though they are present in nature, non-proteinogenic amino acids are usually defined as unnatural or non-natural. Beside their structural diversity, interest in these compounds is due to their occurrence in nature, their biological properties, the analytical aspects, their use as probes, and their incorporation into peptides and proteins, among other reasons. Divided into five convenient sections, Unnatural Amino Acids: Methods and Protocols deals with enzymatic methods used to produce non-natural amino acids, aspects concerning the presence of unnatural amino acids in peptides with antimicrobial properties, genetic incorporation of unnatural amino acids into proteins (yeast and mammalian cells), and detection and quantification of D-amino acids and related enzymes. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Unnatural Amino Acids: Methods and Protocols serves as an ideal guide for scientists and contributes to directing the attention of researchers to the many fields of growing scientific interest in non-natural amino acids.
Book Synopsis Unnatural Reactive Amino Acid Genetic Code Additions by :
Download or read book Unnatural Reactive Amino Acid Genetic Code Additions written by and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.
