Download or read book Structural Tools for the Analysis of Protein nucleic Acid Complexes written by David Malcolm James Lilley and published by Birkhauser. This book was released on 1992 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 2008-04-22 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: The structural biology of protein-nucleic acid interactions is in some ways a mature field and in others in its infancy. High-resolution structures of protein-DNA complexes have been studied since the mid 1980s and a vast array of such structures has now been determined, but surprising and novel structures still appear quite frequently. High-resolution structures of protein-RNA complexes were relatively rare until the last decade. Propelled by advances in technology as well as the realization of RNA's importance to biology, the number of example structures has ballooned in recent years. New insights are now being gained from comparative studies only recently made possible due to the size of the database, as well as from careful biochemical and biophysical studies. As a result of the explosion of research in this area, it is no longer possible to write a comprehensive review. Instead, current review articles tend to focus on particular subtopics of interest. This makes it difficult for newcomers to the field to attain a solid understanding of the basics. One goal of this book is therefore to provide in-depth discussions of the fundamental principles of protein-nucleic acid interactions as well as to illustrate those fundamentals with up-to-date and fascinating examples for those who already possess some familiarity with the field. The book also aims to bridge the gap between the DNA- and the RNA- views of nucleic acid - protein recognition, which are often treated as separate fields. However, this is a false dichotomy because protein - DNA and protein - RNA interactions share many general principles. This book therefore includes relevant examples from both sides, and frames discussions of the fundamentals in terms that are relevant to both. The monograph approaches the study of protein-nucleic acid interactions in two distinctive ways. First, DNA-protein and RNA-protein interactions are presented together. Second, the first half of the book develops the principles of protein-nucleic acid recognition, whereas the second half applies these to more specialized topics. Both halves are illustrated with important real life examples. The first half of the book develops fundamental principles necessary to understand function. An introductory chapter by the editors reviews the basics of nucleic acid structure. Jen-Jacobsen and Jacobsen discuss how solvent interactions play an important role in recognition, illustrated with extensive thermodynamic data on restriction enzymes. Marmorstein and Hong introduce the zoology of the DNA binding domains found in transcription factors, and describe the combinational recognition strategies used by many multiprotein eukaryotic complexes. Two chapters discuss indirect readout of DNA sequence in detail: Berman and Lawson explain the basic principles and illustrate them with in-depth studies of CAP, while in their chapter on DNA bending and compaction Johnson, Stella and Heiss highlight the intrinsic connections between DNA bending and indirect readout. Horvath lays out the fundamentals of protein recognition of single stranded DNA and single stranded RNA, and describes how they apply in a detailed analysis of telomere end binding proteins. Nucleic acids adopt more complex structures - Lilley describes the conformational properties of helical junctions, and how proteins recognize and cleave them. Because RNA readily folds due to the stabilizing role of its 2'-hydroxyl groups, Li discusses how proteins recognize different RNA folds, which include duplex RNA. With the fundamentals laid out, discussion turns to more specialized examples taken from important aspects of nucleic acid metabolism. Schroeder discusses how proteins chaperone RNA by rearranging its structure into a functional form. Berger and Dong discuss how topoisomerases alter the topology of DNA and relieve the superhelical tension introduced by other processes such as replication and transcription. Dyda and Hickman show how DNA transposes mediate genetic mobility and Van Duyne discusses how site-specific recombinases "cut" and "paste" DNA. Horton presents a comprehensive review of the structural families and chemical mechanisms of DNA nucleases, whereas Li in her discussion of RNA-protein recognition also covers RNA nucleases. Lastly, FerrÚ-D'AmarÚ shows how proteins recognize and modify RNA transcripts at specific sites. The book also emphasises the impact of structural biology on understanding how proteins interact with nucleic acids and it is intended for advanced students and established scientists wishing to broaden their horizons.
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 Protein Bioinformatics written by M. Michael Gromiha and published by Academic Press. This book was released on 2011-04-21 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the most pressing tasks in biotechnology today is to unlock the function of each of the thousands of new genes identified every day. Scientists do this by analyzing and interpreting proteins, which are considered the task force of a gene. This single source reference covers all aspects of proteins, explaining fundamentals, synthesizing the latest literature, and demonstrating the most important bioinformatics tools available today for protein analysis, interpretation and prediction. Students and researchers of biotechnology, bioinformatics, proteomics, protein engineering, biophysics, computational biology, molecular modeling, and drug design will find this a ready reference for staying current and productive in this fast evolving interdisciplinary field. Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students.
Download or read book Footprinting of Nucleic Acid Protein Complexes written by and published by Academic Press. This book was released on 2014-05-19 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: Footprinting of Nucleic Acid-Protein Complexes provides protocols for studying the stoichiometry, binding site size and location, and structural changes in nucleic acids caused by their interaction with proteins. The methods are central to studying key biological processes, such as transcription and translation. The techniques are important to experiments in vivoand in vitro, in eukaryotes and in prokaryotes, at qualitative and quantitative levels,and across many disciplines. This book is a laboratory manual of footprinting techniques for studying nucleic acid-protein interactions. It contains clear and concise descriptions of the most important methodologies, and includes in vivo as well as in vitro applications. It is aimed at bench scientists from graduate students on, and should be of value in industrial labs as well as in academic settings. Use of different footprinting approaches can provide unique insights into DNA-protein systems. The protocols containedin this handbook are written to be"user-friendly,"and thus should be conducive to extending the use of footprinting to new systems. The section on quantitative analysis of DNAse I footprints should prove especially useful for in depth evaluation of cooperative interactions. (For the End User) Provides clear exposition of footprinting techniques for characterizing DNA-protein interactions Covers both protection methods for identifying sites of protein binding and interference methods for determining points of contact between DNA and protein Includes approaches for both in vitro and in vivo measurements High quality, timely, and of lasting practical value in the laboratory
Download or read book Protein protein Complexes written by Martin Zacharias and published by World Scientific. This book was released on 2010 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: Given the immense progress achieved in elucidating protein-protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein-protein interactions from the analysis of protein-protein complex structures and interfaces. What are the driving forces for protein-protein association? How can we extract the mechanism of specific recognition from studying protein-protein interfaces? How can this knowledge be used to predict and design protein-protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein-protein interactions, and how can we influence protein-protein interactions by mutagenesis and small-molecule drugs or peptide mimetics?The book consists of about 15 review chapters, written by experts, on the characterization of protein-protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein-protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein-protein complex structures (docking and homology modeling of complexes, etc.) and design of protein-protein interactions. It serves as a bridge between studying/analyzing protein-protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.
Download or read book Protein Protein and Domain Domain Interactions written by Pandjassarame Kangueane and published by Springer. This book was released on 2018-02-16 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book illustrates the importance and significance of the molecular (physical and chemical) and evolutionary (gene fusion) principles of protein-protein and domain-domain interactions towards the understanding of cell division, disease mechanism and target definition in drug discovery. It describes the complex issues associated with this phenomenon using cutting edge advancement in Bioinformatics and Bioinformation Discovery. The chapters provide current information pertaining to the types of protein-protein complexes (homodimers, heterodimers, multimer complexes) in context with various specific and sensitive biological functions. The significance of such complex formation in human biology in the light of molecular evolution is also highlighted using several examples. The chapters also describe recent advancements on the molecular principles of protein-protein interaction with reference to evolution towards target identification in drug discovery. Finally, the book also elucidates a comprehensive yet a representative description of a large number of challenges associated with the molecular interaction of proteins.
Download or read book The Definitive Guide to MongoDB written by Peter Membrey and published by Apress. This book was released on 2011-01-27 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: MongoDB, a cross-platform NoSQL database, is the fastest-growing new database in the world. MongoDB provides a rich document-oriented structure with dynamic queries that you’ll recognize from RDBMS offerings such as MySQL. In other words, this is a book about a NoSQL database that does not require the SQL crowd to re-learn how the database world works! MongoDB has reached 1.0 and boasts 50,000+ users. The community is strong and vibrant and MongoDB is improving at a fast rate. With scalable and fast databases becoming critical for today’s applications, this book shows you how to install, administer and program MongoDB without pretending SQL never existed.
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Chemistry of Protein Conjugation and Cross Linking written by Shan S. Wong and published by CRC Press. This book was released on 1991-06-18 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical cross-linking reagents have attained great practical use in industry as well as in basic research, and an understanding of their fundamental principles of reaction is paramount to their applications. With broad coverage of the development and application of these reagents, Chemistry of Protein Conjugation and Cross-Linking discusses the mechanism of reaction and allows you to put the theory into practice. The book offers an explanation of the underlying mechanism of chemical modification, surveys all the bifunctional reagents used in bioconjugation and cross-linking, and provides a review of practical applications of these reagents in various areas of biochemistry, molecular biology, biotechnology, nucleic acid chemistry, immunochemistry, and diagnostic and biomedical disciplines. It contains numerous examples and illustrations, plus step-by-step explanations to reaction procedures. It is an excellent introduction and a comprehensive reference about chemical modification.
Download or read book Structural and Biochemical Analysis of Selected Nucleic Acid protein Complexes written by Christina Schmidt and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Circular Dichroism and the Conformational Analysis of Biomolecules written by G.D. Fasman and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 739 pages. Available in PDF, EPUB and Kindle. Book excerpt: ''Excellent and very timely....It will undoubtedly become a standard reference for the application of circular dichroism (CD) to biomolecules.'' --- Quarterly Review of Biology, March 1997 ''[T]estament to the book's utility is the fact that during the course of my review I had to 'rescue' it from the desks of graduate students on an almost daily basis. In summary, this is a great book.'' --- American Scientist ''Well documented chapters provide a very good insight into the problems surrounding the conformation of biomacromolecules...An indispensible source of information.'' --- Nahrung, 42(2), 1998 Renowned experts present the first state-of-the-art description of circular dichroism spectroscopy (CD). Chapters present in-depth discussions of the history of the field, the theory of CD for application to globular proteins, membrane proteins, peptides, nucleic acids and their interactions, carbohydrates, and instrumentation. Discussions also feature new techniques using synchrotron radiation, vibrational Raman optical activity, and vibrational CD. More than 250 illustrations supplement the text.
Download or read book Structural Bioinformatics written by Jenny Gu and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 1105 pages. Available in PDF, EPUB and Kindle. Book excerpt: Structural Bioinformatics was the first major effort to show the application of the principles and basic knowledge of the larger field of bioinformatics to questions focusing on macromolecular structure, such as the prediction of protein structure and how proteins carry out cellular functions, and how the application of bioinformatics to these life science issues can improve healthcare by accelerating drug discovery and development. Designed primarily as a reference, the first edition nevertheless saw widespread use as a textbook in graduate and undergraduate university courses dealing with the theories and associated algorithms, resources, and tools used in the analysis, prediction, and theoretical underpinnings of DNA, RNA, and proteins. This new edition contains not only thorough updates of the advances in structural bioinformatics since publication of the first edition, but also features eleven new chapters dealing with frontier areas of high scientific impact, including: sampling and search techniques; use of mass spectrometry; genome functional annotation; and much more. Offering detailed coverage for practitioners while remaining accessible to the novice, Structural Bioinformatics, Second Edition is a valuable resource and an excellent textbook for a range of readers in the bioinformatics and advanced biology fields. Praise for the previous edition: "This book is a gold mine of fundamental and practical information in an area not previously well represented in book form." —Biochemistry and Molecular Education "... destined to become a classic reference work for workers at all levels in structural bioinformatics...recommended with great enthusiasm for educators, researchers, and graduate students." —BAMBED "...a useful and timely summary of a rapidly expanding field." —Nature Structural Biology "...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." —Briefings in Bioinformatics
Download or read book Development of Experimental Techniques to Study Protein and Nucleic Acid Structures written by and published by . This book was released on 1996 with total page 6 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). This research project sought to develop experimental tools for structural biology, specifically those applicable to three-dimensional, biomolecular-structure analysis. Most biological systems function in solution environments, and the ability to study proteins and polynucleotides under physiologically relevant conditions is of paramount importance. The authors have therefore adopted a three-pronged approach which involves crystallographic and nuclear magnetic resonance (NMR) spectroscopic methods to study protein and DNA structures at high (atomic) resolution as well as neutron and x-ray scattering techniques to study the complexes they form in solution. Both the NMR and neutron methods benefit from isotope labeling strategies, and all provide experimental data that benefit from the computational and theoretical tools being developed. The authors have focused on studies of protein-nucleic acid complexes and DNA hairpin structures important for understanding the regulation of gene expression, as well as the fundamental interactions that allow these complexes to form.
Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. Presents a thorough overview of the latest and emerging methods and technologies for protein study Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy Includes computational and machine learning methods Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
Download or read book Structure Methods DNA protein complexes proteins written by Ramaswamy H. Sarma and published by . This book was released on 1990 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Principles of Nucleic Acid Structure written by Stephen Neidle and published by Academic Press. This book was released on 2021-10-15 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: Principles of Nucleic Acid Structure, Second Edition, provides the most complete and concise summary of underlying principles and approaches to studying nucleic acid structure, including discussions of X-ray crystallography, NMR, molecular modelling and databases. The book's focus is on a survey of structures that are especially important for biomedical research and pharmacological applications. This updated edition includes the latest advances relevant to recognition of DNA and RNA by small molecules and proteins, including sections on RNA folding, ribosome structure and antibiotic interactions, DNA quadruplexes, DNA and RNA protein complexes and short interfering RNA (siRNA). This reference is a must-have for those seeking an authoritative, comprehensive and up-to-date source on all aspects of nucleic acid structure, from basic first principles to details of recent research results. Completely updated, with an expanded section on protein-nucleic acid interactions that reflects major increases in our knowledge Defines technical terms for novices Includes a complete list of resources, including relevant online databases and software, as well as useful websites
