Download or read book Crystallographic Studies of the E Coli DNA Replication Restart Primosome written by Aude Izaac and published by . This book was released on 2005 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the mechanisms of DNA replication has been one of the main research topics in biochemistry for decades, due to the tremendous potential applications involved, such as medical treatments and better knowledge of the biological evolution of organisms. In this perspective, macromolecular X ray crystallography provides a very powerful tool. By solving the 3 dimensional structure of the proteins involved in replication mechanisms, one can get a good insight at complicated biological systems at the atomic level. It is also important to study the protein-protein and protein-substrate interactions when they form biological complexes. This work focused on studying several proteins which are associated with the assembly of the replication restart primosome in Escherichia coli, during the repair of damaged DNA. The crystallization of PriA, the most important of the restart primosome proteins, was investigated. Two truncations of PriA (the PriA N and PriA NI domains) were expressed, purified and characterized to be prepared for crystallization. Three additional replication restart proteins: PriB, PriC and DnaT, were expressed and purified. The solubility of each protein was optimized by identifying the best solution conditions. The proteins were characterized, alone and in complexes, using several biophysical techniques. DnaT was successfully crystallized and screened for X-ray diffraction. Finally, using ten standard test proteins, the correlation between the optimization of protein solubility (and solution conditions) and the success of crystal screening was studied.
Download or read book Cellular Contexts and Biochemical Mechanisms of Dna Replication Restart in Escherichia Coli written by Aidan Mair McKenzie and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Before cells can divide, they must first duplicate their genome through DNA replication. DNA replication is facilitated by the coordinated activities of multiprotein complexes (replisomes). While the speed and abilities of replisomes are mystifying, they are frequently met with challenges to their progression. During active replication, Escherichia coli replisomes are estimated to physically dissociate from the genome at least once per cell cycle after colliding with DNA damage or tightly associated proteins. To sustain cellular viability, DNA replication needs to be reinitiated at these abandoned replication forks through the process of DNA replication restart. Here, I present a genetic, biochemical, and structural investigation of DNA replication restart in E. coli to better define its cellular role and mechanistic details. In Chapter 1, I outline the original discovery of replication restart proteins (RRPs) and the evidence used to propose a three-pathway model for DNA replication restart in E. coli (consisting of the PriA/PriB, PriA/PriC, and PriC/Rep pathways). To facilitate replication restart, each pathway recognizes an abandoned replication fork, remodels the fork, recruits additional RRPs, and ultimately reloads the replicative helicase (DnaB) onto the DNA with the help of its helicase loader (DnaC). Chapter 2 describes a genetic study that systematically defined the roles of specific replication restart pathways in a variety of cellular environments. My results helped integrate DNA replication restart within other cellular processes by revealing a tight link between the repair of double-strand breaks and the PriA/PriB restart pathway. In Chapter 3, I exploited a streamlined DnaB reloading system afforded by PriC to structurally define its manner of binding to the replicative helicase/loader (DnaB6/DnaC6) complex. The cryoEM structure identified dramatic conformational changes required to satisfy the binding interface between PriC and DnaB, and subsequent biochemical investigation identified a hydrophobic packing interface as important for sustained binding. A summary of the findings in Chapters 2 and 3, as well as future directions, are provided in Chapter 4. This work probed mechanistic details of DNA replication restart in E. coli by revealing the cellular processes (and missteps) that necessitate replication restart and helped define the biochemical mechanism of PriC-mediated replicative helicase loading.
Download or read book Studies on the DNA Helicase Activities of the Escherichia Coli Primosome written by Myung Soo Lee and published by . This book was released on 1989 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structural Studies on the DNA Replication Apparatus written by Brian Douglas Guenther and published by . This book was released on 1996 with total page 235 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Study on the Molecular Interaction Between Escherichia Coli Single stranded DNA Binding Protein and Its Partner Protein in DNA Replication Restart written by and published by . This book was released on 2021 with total page 77 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Crystallographic Studies on the Purine Repressor an Escherichia Coli DNA binding Protein written by Maria A. Schumacher and published by . This book was released on 1995 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2008 with total page 1006 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA Helicases and DNA Motor Proteins written by Maria Spies and published by Springer Science & Business Media. This book was released on 2012-11-19 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, a number of groundbreaking structural and mechanistic studies deepened our understanding of helicase mechanisms and established new approaches for their analyses. Many fundamental mechanistic questions ranging from the mechanism of force generation, mechanochemical coupling to distinct mechanisms by which the same enzyme translocates on DNA removing obstacles, unwinds DNA and/or remodels nucleoprotein complexes, however, remain to be answered. It is even less understood how the helicase motors are incorporated into a wide range of genome maintenance and repair machines. The field has reached a stage when the studies of molecular mechanisms and basic biology of helicases can and shall be integrated with the studies of development, cancer and longevity. The objective of this book is to provide the first systematic overview of structure, function and regulation of DNA helicases and related molecular motors. By integrating the knowledge obtained through the diverse technical approaches ranging from single-molecule biophysics to cellular and molecular biological studies the editors aim to provide a unified view on how helicases function in the cell, are regulated in response to different cellular stresses and are integrated into large macromolecular assemblies to form a complex and adaptive living system.
Download or read book Molecular Genetics of Recombination written by Andrés Aguilera and published by Springer Science & Business Media. This book was released on 2007-04-24 with total page 536 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work offers a fascinating insight into a crucial genetic process. Recombination is, quite simply, one of the most important topics in contemporary biology. This book is a totally comprehensive treatment of the subject, summarizing all existing views on the topic and at the same time putting them into context. It provides in-depth and up-to-date analysis of the chapter topics, and has been written by international experts in the field.
Download or read book Bacteriophage T4 written by Christopher K. Mathews and published by . This book was released on 1983 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA Replication Recombination and Repair written by Fumio Hanaoka and published by Springer. This book was released on 2016-01-22 with total page 548 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a comprehensive review of the detailed molecular mechanisms of and functional crosstalk among the replication, recombination, and repair of DNA (collectively called the "3Rs") and the related processes, with special consciousness of their biological and clinical consequences. The 3Rs are fundamental molecular mechanisms for organisms to maintain and sometimes intentionally alter genetic information. DNA replication, recombination, and repair, individually, have been important subjects of molecular biology since its emergence, but we have recently become aware that the 3Rs are actually much more intimately related to one another than we used to realize. Furthermore, the 3R research fields have been growing even more interdisciplinary, with better understanding of molecular mechanisms underlying other important processes, such as chromosome structures and functions, cell cycle and checkpoints, transcriptional and epigenetic regulation, and so on. This book comprises 7 parts and 21 chapters: Part 1 (Chapters 1–3), DNA Replication; Part 2 (Chapters 4–6), DNA Recombination; Part 3 (Chapters 7–9), DNA Repair; Part 4 (Chapters 10–13), Genome Instability and Mutagenesis; Part 5 (Chapters 14–15), Chromosome Dynamics and Functions; Part 6 (Chapters 16–18), Cell Cycle and Checkpoints; Part 7 (Chapters 19–21), Interplay with Transcription and Epigenetic Regulation. This volume should attract the great interest of graduate students, postdoctoral fellows, and senior scientists in broad research fields of basic molecular biology, not only the core 3Rs, but also the various related fields (chromosome, cell cycle, transcription, epigenetics, and similar areas). Additionally, researchers in neurological sciences, developmental biology, immunology, evolutionary biology, and many other fields will find this book valuable.
Download or read book Proteins written by David Whitford and published by John Wiley & Sons. This book was released on 2013-04-25 with total page 544 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins: Structure and Function is a comprehensive introduction to the study of proteins and their importance to modern biochemistry. Each chapter addresses the structure and function of proteins with a definitive theme designed to enhance student understanding. Opening with a brief historical overview of the subject the book moves on to discuss the ‘building blocks’ of proteins and their respective chemical and physical properties. Later chapters explore experimental and computational methods of comparing proteins, methods of protein purification and protein folding and stability. The latest developments in the field are included and key concepts introduced in a user-friendly way to ensure that students are able to grasp the essentials before moving on to more advanced study and analysis of proteins. An invaluable resource for students of Biochemistry, Molecular Biology, Medicine and Chemistry providing a modern approach to the subject of Proteins.
Download or read book Iron Sulfur Clusters in Chemistry and Biology written by Tracey Rouault and published by Walter de Gruyter GmbH & Co KG. This book was released on 2014-08-20 with total page 672 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume on iron-sulfur proteins includes chapters that describe the initial discovery of iron-sulfur proteins in the 1960s to elucidation of the roles of iron sulfur clusters as prosthetic groups of enzymes, such as the citric acid cycle enzyme, aconitase, and numerous other proteins, ranging from nitrogenase to DNA repair proteins. The capacity of iron sulfur clusters to accept and delocalize single electrons is explained by basic chemical principles, which illustrate why iron sulfur proteins are uniquely suitable for electron transport and other activities. Techniques used for detection and stabilization of iron-sulfur clusters, including EPR and Mossbauer spectroscopies, are discussed because they are important for characterizing unrecognized and elusive iron sulfur proteins. Recent insights into how nitrogenase works have arisen from multiple advances, described here, including studies of high-resolution crystal structures. Numerous chapters discuss how microbes, plants, and animals synthesize these complex prosthetic groups, and why it is important to understand the chemistry and biogenesis of iron sulfur proteins. In addition to their vital importance in mitochondrial respiration, numerous iron sulfur proteins are important in maintenance of DNA integrity. Multiple rare human diseases with different clinical presentations are caused by mutations of genes in the iron sulfur cluster biogenesis pathway. Understanding iron sulfur proteins is important for understanding a rapidly expanding group of metabolic pathways important in all kingdoms of life, and for understanding processes ranging from nitrogen fixation to human disease.
Download or read book Bacterial Conjugation written by D.B. Clewell and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial plasmids originating in a wide range of genera are being studied from a variety of perspectives in hundreds of laboratories around the globe. These elements are well known for carrying "special" genes that confer important survival properties, frequently neces sary under atypical conditions. Classic examples of plasmid-borne genes are those provid ing bacterial resistance to toxic substances such as antibiotics, metal ions, and bacte riophage. Often included are those determining bacteriocins, which may give the bacterium an advantage in a highly competitive environment. Genes offering metabolic alternatives to the cell under nutritionally stressed conditions are also commonly found on plasmids, as are determinants important to colonization and pathogenesis. It is likely that in many, if not most, cases plasmids and their passenger determinants represent DNA acquired recently by their bacterial hosts, and it is the characteristic mobility of these elements that enables their efficient establishment in new bacterial cells by the process known as conjugation. Whereas many plasmids are fully capable of promoting their own conjugal transfer, others move only with help from coresident elements. The ability of a plasmid to establish itself in a variety of different species is com mon, and recent studies have shown that transfer can in some cases occur from bacterial cells to eukaryotes such as yeast.
Download or read book Student Companion to Accompany Fundamentals of Biochemistry written by Akif Uzman and published by Wiley. This book was released on 2012-01-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Voet and Pratt's 4th edition of Principles of Biochemistry, challenges readers to better understand the chemistry behind the biological structure and reactions occurring in living systems. The latest edition continues this tradition, and additionally incorporates coverage of recent research and an expanded focus on preparing and supporting students throughout the course. With the addition of new conceptual assessment content to WileyPLUS, providing the opportunity to assess conceptual understanding of key introductory biochemistry concepts and retrain themselves on their misconceptions WileyPLUS sold separately from text.
Download or read book American Doctoral Dissertations written by and published by . This book was released on 1998 with total page 784 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Chemical and Synthetic Biology Approaches to Understand Cellular Functions Part C written by and published by Academic Press. This book was released on 2020-02-10 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical and Synthetic Biology Approaches to Understand Cellular Functions - Part C, Volume 633, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial. This release includes sections on Next generation probes for molecular imaging in cells, Competitive binding assay for biotin and biotin derivatives, based on avidin and biotin-4-fluorescein, Converting avidin to bind ligands other than biotin, especially steroids, Chemoenzymatic Labeling Strategy, Engineered Siderophores, Small molecules to inhibit bacterial population behavior, NMR tube bioreactor, Small molecule controlled RAS activation system, Small molecule regulated Cas9, the Design and application of synthetic receptors, and much more. - Contains the authority of authors who are leaders in their field - Provides a comprehensive source on new methods and research in enzymology
