Download or read book Kinetic Gating Mechanism of DNA Damage Recognition by Rad4 XPC written by and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Lastly, kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.
Download or read book Dynamics and Mechanism of DNA Bending Proteins in Binding Site Recognition written by Yogambigai Velmurugu and published by Springer. This book was released on 2016-11-29 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: Using a novel approach that combines high temporal resolution of the laser T-jump technique with unique sets of fluorescent probes, this study unveils previously unresolved DNA dynamics during search and recognition by an architectural DNA bending protein and two DNA damage recognition proteins. Many cellular processes involve special proteins that bind to specific DNA sites with high affinity. How these proteins recognize their sites while rapidly searching amidst ~3 billion nonspecific sites in genomic DNA remains an outstanding puzzle. Structural studies show that proteins severely deform DNA at specific sites and indicate that DNA deformability is a key factor in site-specific recognition. However, the dynamics of DNA deformations have been difficult to capture, thus obscuring our understanding of recognition mechanisms. The experiments presented in this thesis uncover, for the first time, rapid (~100-500 microseconds) DNA unwinding/bending attributed to nonspecific interrogation, prior to slower (~5-50 milliseconds) DNA kinking/bending/nucleotide-flipping during recognition. These results help illuminate how a searching protein interrogates DNA deformability and eventually “stumbles” upon its target site. Submillisecond interrogation may promote preferential stalling of the rapidly scanning protein at cognate sites, thus enabling site-recognition. Such multi-step search-interrogation-recognition processes through dynamic conformational changes may well be common to the recognition mechanisms for diverse DNA-binding proteins.
Download or read book DNA Damage Recognition written by Wolfram Siede and published by CRC Press. This book was released on 2005-09-19 with total page 871 pages. Available in PDF, EPUB and Kindle. Book excerpt: Stands as the most comprehensive guide to the subject-covering every essential topic related to DNA damage identification and repair. Covering a wide array of topics from bacteria to human cells, this book summarizes recent developments in DNA damage repair and recognition while providing timely reviews on the molecular mechanisms employe
Download or read book Mechanisms of DNA Damage Recognition in Mammalian Cells written by Hanspeter Naegeli and published by Springer Science & Business Media. This book was released on 2013-11-21 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Mechanism of Versatile DNA Damage Recognition by Xeroderma Pigmentosum Group C XPC Protein written by Flurina Christina Clement Frey and published by . This book was released on 2010 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Single Molecule Studies of Rad4 Rad23 Reveal a Dynamic DNA Damage Recognition Process written by Muwen Kong and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Role of DNA Damage Dependent Rad23 Ubiquination in Stabilization of Rad4 written by Archana Schrestha and published by . This book was released on 2011 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nucleotide Excision Repair (NER) is a major DNA repair mechanism after UV light exposure. Rad23 in combination with Rad4, Nucleotide Excision Repair Factor 2 (NEF2), play a critical role in DNA damage recognition. Mutation or loss of the RAD4 human homolog, XPC, can lead to a serious disorder, Xeroderma Pigmentosum, which is characterized by increased sensitivity to sunlight and predisposition to cancer. Little is known about how Rad23 can function in both these roles and what signals are needed to stabilize a protein verses send it to the proteasome for degradation. Current research in Dr. Smith's lab has shown that the ubiquitin like (UBL) domain of Rad23 is often found to be ubiquitinated after UV light exposure which coincides with the increased level of Rad4. The objective of this project is to determine if the ubiquitination on Rad23 is involved in Rad4 stabilization in yeast, Saccharomyces. In order to determine the site of UV-dependent ubiquitin modification within the UBL domain of Rad23, 14 lysine residues were replaced by arginine individually as well as in various combinations. Molecular techniques such as UV sensitivity assays and western blots were applied to study the functional properties of these Rad23 mutants in Saccharomyces, and the role of ubiquitination following UV exposure. The site directed mutagenesis performed in this study has reiterated the importance of UBL domain since the combination mutants (lysine substituted by arginine) were UV sensitive.
Download or read book DNA Repair written by and published by Academic Press. This book was released on 2019-10-16 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Repair, Volume 45 in The Enzymes series highlights new advances in the field, with this new volume presenting interesting chapters on DNA polymerase beta and other gap-filling enzymes in mammalian base excision repair, Translesion polymerases, mechanism and function, The Rev1-Pol? Mutasome: Structure and Interactions in Translesion Synthesis, Challenges for base excision repair enzymes: acquiring access to damaged DNA in chromatin Nucleotide excision repair, DNA damage recognition mechanisms in mammalian nucleotide excision repair, Advances in understanding DNA mismatch repair, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in The Enzymes series
Download or read book DNA Repair Disorders written by Chikako Nishigori and published by Springer. This book was released on 2018-12-31 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the clinical aspects of DNA repair disorders. Nucleotide excision repair is an important pathway for humans, as it is involved in biologically fundamental functions. This work presents clinical features together with the pathogenesis of DNA repair disorders such as Xertoderma Pigmentosum (XP). Studies on animal models are included as well. Clinical feature characteristics of each clinical subtype of XP are depicted according to the genotype, giving accurate and detailed information about the clinical features in terms of gene alterations, change of protein structure, and dysfunction in some of the repair pathways. This book is unique in that it provides detailed information on clinical features from more than 100 patients with XP-A, which is characterized by very severe manifestation of skin photosensitivity and neurological dysfunction. It will give readers important knowledge for understanding the concept and molecular mechanisms of DNA repair disorders. It also describes how to treat and care for patients with XP based on vast experience in clinical practice. DNA Repair Disorders will be a useful resource not only for physicians and basic scientists who are interested in and/or take care of patients with DNA repair disorders, but also dermatologists, neurologists, and researchers in the field of radiation biology and photobiology.
Download or read book The Chemical Biology of DNA Damage written by Nicholas E. Geacintov and published by John Wiley & Sons. This book was released on 2011-08-04 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bringing the power of biochemical analysis to toxicology, this modern reference explains genotoxicity at the molecular level, showing the links between a DNA lesion and the resulting cellular or organismic response. Clearly divided into two main sections, Part 1 focuses on selected examples of important DNA lesions and their biological impact, while the second part covers current advances in assessing and predicting the genotoxic effects of chemicals, taking into account the biological responses mediated by the DNA repair, replication and transcription machineries. A ready reference for biochemists, toxicologists, molecular and cell biologists, and geneticists seeking a better understanding of the impact of chemicals on human health.
Download or read book Protein Nucleic Acid Interactions written by Phoebe A. Rice and published by Royal Society of Chemistry. This book was released on 2008-05-22 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides both in-depth background and up-to-date information in this area. The chapters are organized by general themes and principles, written by experts who illustrate topics with current findings. Topics covered include: - the role of ions and hydration in protein-nucleic acid interactions - transcription factors and combinatorial specificity - indirect readout of DNA sequence - single-stranded nucleic acid binding proteins - nucleic acid junctions and proteins, - RNA protein recognition - recognition of DNA damage. It will be a key reference for both advanced students and established scientists wishing to broaden their horizons.
Download or read book Biophysics of DNA Protein Interactions written by Mark C. Williams and published by Springer. This book was released on 2012-12-05 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists. The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.
Download or read book Cilia Part B written by and published by Academic Press. This book was released on 2013-04-16 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers cilia and includes chapters on such topics as methods for studying ciliary polarity in Xenopus, analysis of signaling pathways in mammalian spermatozoa, and biochemical and physiological analysis of axonemal dyneins.
Download or read book Protein nucleic Acid Interaction written by Wolfram Saenger and published by . This book was released on 1989 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains a series of essays which describe a range of problems in the field of nucleic-acid interactions, investigated by a variety of techniques. An introductory chapter on DNA-protein interactions in the regulation of gene expression is followed by papers on selected model systems.
Download or read book Networking for Nerds written by Alaina G. Levine and published by John Wiley & Sons. This book was released on 2015-05-13 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: Networking for Nerds provides a step-by-step guide to understanding how to access hidden professional opportunities through networking. With an emphasis on practical advice on how and why to network, you will learn how to formulate and execute a strategic networking plan that is dynamic, multidimensional, and leverages social media platforms and other networking channels. An invaluable resource for both established and early-career scientists and engineers (as well as networking neophytes!), Networking for Nerds offers concrete insight on crafting professional networks that are mutually beneficial and support the advancement of both your career goals and your scholarly ambitions. “Networking” does not mean going to one reception or speaking with a few people at one conference, and never contacting them again. Rather, “networking” involves a spectrum of activities that engages both parties, ensures everyone’s value is appropriately communicated, and allows for the exploration of a win-win collaboration of some kind. Written by award-winning entrepreneur and strategic career planning expert Alaina G. Levine, Networking for Nerds is an essential resource for anyone working in scientific and engineering fields looking to enhance their professional planning for a truly fulfilling, exciting, and stimulating career. professional planning for a truly fulfilling, exciting, and stimulating career.Networking for Nerds provides a step-by-step guide to understanding how to access hidden professionalopportunities through networking. With an emphasis on practical advice on how and why to network, youwill learn how to formulate and execute a strategic networking plan that is dynamic, multidimensional, andleverages social media platforms and other networking channels.An invaluable resource for both established and early-career scientists and engineers (as well as networkingneophytes!), Networking for Nerds offers concrete insight on crafting professional networks that aremutually beneficial and support the advancement of both your career goals and your scholarly ambitions.“Networking” does not mean going to one reception or speaking with a few people at one conference, andnever contacting them again. Rather, “networking” involves a spectrum of activities that engages bothparties, ensures everyone’s value is appropriately communicated, and allows for the exploration of a win-wincollaboration of some kind.Written by award-winning entrepreneur and strategic career planning expert Alaina G. Levine, Networking forNerds is an essential resource for anyone working in scientific and engineering fields looking to enhance theirprofessional planning for a truly fulfilling, exciting, and stimulating career.
Download or read book Photochemistry written by Angelo Albini and published by Royal Society of Chemistry. This book was released on 2019-09-27 with total page 546 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drawing on the continued wealth of photochemical research, this volume combines reviews on the latest advances in the field with specific topical highlights. Starting with periodical reports of the recent literature on physical and inorganic aspects, light induced reactions in cryogenic matrices, properties of transition-metal compounds, time-resolved spectroscopy, the exploitation of solar energy and the molecules of colour. Coverage continues with highlighted topics, in the second part, from photoresponsive hydrogels, the tunable photoredox properties of organic dyes, light-driven asymmetric organocatalytic processes, dual gold–photoredox catalysis, the preparation and characterization of photosensitizers for triplet–triplet annihilation photon upconversion and the role of photochemistry on traditional synthetic processes. This volume will include for the first time a section entitled ‘SPR Lectures on Photochemistry’, providing examples for academic readers to introduce a photochemistry topic and precious help for students in photochemistry. Providing critical analysis of the topics, this book is essential reading for anyone wanting to keep up to date with the literature on photochemistry and its applications.
Download or read book Understanding Xeroderma Pigmentosum written by and published by . This book was released on 1995 with total page 22 pages. Available in PDF, EPUB and Kindle. Book excerpt:
