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Multiscale Modeling Of Dna From Double Helix To Chromatin
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Book Synopsis Multiscale Modeling of DNA, from Double-helix to Chromatin by : Sam Meyer
Download or read book Multiscale Modeling of DNA, from Double-helix to Chromatin written by Sam Meyer and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the nucleus of eukaryotic cells, DNA wraps around histone proteins to form nucleosomes, which in turn associate in a compact and dynamic fiber called chromatin. The physical properties of this fiber at different lengthscales, from the DNA double-helix to micrometer-sized chromosomes, are essential to the complex mechanisms of gene expression and its regulation. The present thesis is a contribution to the development of physical models, which are able to link different scales and to interpret and integrate data from a wide range of experimental and computational approaches. In the first part, we use Molecular Dynamics simulations of DNA oligomers to study doublehelical DNA at different temperatures. We estimate the sequence-dependent contribution of entropy to DNA elasticity, in relation with recent experiments on DNA persistence length. In the second part, we model the DNA-histone interactions within the nucleosome core particle,using DNA nanomechanics to extract a force field from a set of crystallographic nucleosome structures and Molecular Dynamics snapshots. In the third part, we consider the softer part of the nucleosome, the linker DNA between coreparticles which transiently associates with the histone H1 to form a “stem”.We combine existing structural knowledge with experimental data at two different resolutions (DNA footprints and electro-micrographs) to develop a nanoscale model of the stem.
Book Synopsis Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events by : Fabio Trovato
Download or read book Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events written by Fabio Trovato and published by Frontiers Media SA. This book was released on 2022-01-11 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations by : Valentina Tozzini
Download or read book Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations written by Valentina Tozzini and published by Frontiers Media SA. This book was released on 2020-10-27 with total page 235 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Book Synopsis Revealing DNA Dynamics from Atomistic to Genomic Level by Multiscale Computational Approaches by : Jürgen Walther
Download or read book Revealing DNA Dynamics from Atomistic to Genomic Level by Multiscale Computational Approaches written by Jürgen Walther and published by . This book was released on 2019 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The study of DNA from atomistic to mesoscopic level and connecting different resolution levels constitutes a major challenge since the new millennium. In the early 2000s, experiments could resolve for the first time the structure of the nucleosome in high detail or capture physical contacts in the genome of segments far apart in sequence. At around the same time, the force field development for atomistic nucleic acid simulations reached a peak with parmbsc0 in 2007 and coarse grain nucleosome fiber models emerged. The first decade ended with a remarkable experimental advance in visualizing the whole genome, Hi-C. In the current decade, almost ten years after Hi-C was invented, the structure of the cell nucleus is still a very hot topic. We can now harvest the fruits of the pioneers in the first decade of multi-scale investigation of DNA and connect the different resolution levels to obtain a complete picture of DNA from electron orbitals to genome folding. In this work, we use computational approaches to dissect the different resolution levels, from atomistic MD simulations to mesoscopic secondary chromatin structure modeling. We developed a force-field (parmbsc1) for the accurate description of atomistic DNA dynamics based on quantum mechanical simulations. With the accuracy of parmbsc1, sequence-dependent effects of B-DNA flexibility beyond the base pair level were described and used as a starting point to parametrize a novel helical coarse grain model which shows similar accuracy to the DNA dynamics obtained by atomistic MD, but at much lower computational cost. In a newly developed nucleosome fiber model the coarse grain DNA algorithm is used for the linker DNA description and alongside with a simple mesoscopic characterization of the nucleosome chromatin dynamics can be probed at kilobase scale with a DNA model whose roots lie in the quantum mechanical regime. On top of that, to meet current standards of accessibility and usability of tools, the developed coarse grain DNA and nucleosome fiber model are freely available as stand-alone versions or integrated in a single webserver or large-scale online research environment platform." -- TDX.
Book Synopsis Coarse-Grained Modeling of Biomolecules by : Garegin A. Papoian
Download or read book Coarse-Grained Modeling of Biomolecules written by Garegin A. Papoian and published by CRC Press. This book was released on 2017-10-30 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.
Book Synopsis The Packaging of DNA in Chromatin by : Guohui Zheng
Download or read book The Packaging of DNA in Chromatin written by Guohui Zheng and published by . This book was released on 2010 with total page 191 pages. Available in PDF, EPUB and Kindle. Book excerpt: The mechanical properties of DNA play a key role in its biological processing, determining how the long, thin, double-helical molecule responds to the binding of proteins and functions in confined spaces within a cell. In eukaryotes, about 75-90% of genomic DNA exists in the form of nucleosomes, which are the fundamental units of DNA packaging in chromatin and the primary determinate of DNA accessibility. The structure of chromatin undergoes various changes that depend, at least in part, upon the requirements of gene expression and other functional environments. The dynamics of DNA packaging in chromatin is thus fundamental to numerous biological processes. The flexibility of DNA is important in packaging DNA over lengths comparable to its persistence length during genetic processing and the sequence-dependent properties of DNA determine the positioning of nucleosomes in the genome and the sites of binding of enzymes and transcription factors. In addition, understanding the correlation between DNA flexibility and histone-DNA interactions inside the nucleosome is essential for unraveling currently unsolved mechanisms of gene regulation. Furthermore, although many experimental techniques have emerged to examine the overall structure of chromatin fibers, the internal arrangement of DNA and histones remains unclear. Thus an appropriate computational model able to incorporate experimental observations is key to interpretation of the folding and unfolding of chromatin. The major goal of this thesis is to understand some of biophysical mechanisms involved in the packaging of DNA into chromatin using computational techniques at multi-scales: (i) to determine the sequence-dependent flexibility of DNA by developing DNA deformation analysis tools and databases; (ii) to design DNA spatial configurations using knowledge-based Monte-Carlo sampling; (iii) to map protein-DNA recognition inside nucleosomes in terms of realistic molecular treatments; and (iv) to interpret the internal structure of chromatin fibers and examine chromatin looping using novel modeling and simulation methods.
Book Synopsis Organization of DNA in Chromatin by : Henry Sobell
Download or read book Organization of DNA in Chromatin written by Henry Sobell and published by . This book was released on 2023-01-25 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: As the DNA in our genome comprises about three billion base-pairs, with each base-pair separated by a third of a nanometer - its total length is about a meter - of all which residing within a compact form knows as chromatin. At first guess, one might think the DNA to be a wound up like a ball of yarn, but chromatin turns out to be a more complex structure, DNA being organized into hierarchical series of superhelices. Counting the right-handed double-helix as the first stage in the hierarchical ordering, the second consists of 147 base-pairs wound around the outside of nucleosomes as a left-handed toroidal-superhelix containing one and three-quarter turns. Each nucleosome contains two pairs each of four different histones, small positively charged basic proteins called H2A, H2B, H3 and H4 spatially related by two-fold symmetry. Adjacent nucleosomes remain connected together by linker DNA, additional DNA (variable in length, but generally between 5- to 60 base-pairs) that exists between nucleosomes, resulting in the formation of an extended 100 Angstrom fiber. In the presence of an additional histone (H1), DNA is known to undergo a still higher level of compaction, organizing itself into a solenoidal super helical structure having a diameter of about 300 Angstroms. This 300 Angstrom fiber can readily be seen by electron microscopy and, almost certainly, the unraveling of its structure foreshadows still further complex structural features of chromatin to be discovered in future years. In order for DNA to be organized into this hierarchical series of superhelices, there must be a source of flexibility in DNA structure that allows this to happen. Earlier, the author put forward a kinked model to understand how DNA is organized within the nucleosome. The model assumed nucleosome DNA to be in its B- form, separated by 'mixed-puckered kinks' every 10 base-pairs. Ink this book, he presents a modification to this model; this being necessary to explain important additional experimental information uncovered several years after the model was proposed. The modified model proposed that if there were an equal probability of both 10 base-pars of B- DNA or 11 base-pairs of A- DNA existing within any given segment of the left-handed toroidal super helical structure - these being connected together by 'mixed-puckered kinks' - then a population of such aperiodic structures can be expected to give rise to the periodic cutting-patterns observed experimentally. This would be true for naked DNA molecules immobilized on a calcium-phosphate crystalline surface as well, provided they also formed left-handed toroidal superhelices under these conditions. In both cases, probability considerations predict cutting patters to be symmetrically distributed around integral multiples of 10.5 base-pairs along DNA, the relative magnitudes of the surroundings peaks in these patterns being governed by the binomial distribution - the proof of which is presented in this book.
Book Synopsis Nuclear Organization and Function by : Terri Grodzicker
Download or read book Nuclear Organization and Function written by Terri Grodzicker and published by . This book was released on 2011 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is based on presentations by the world-renowned investigators who gathered at the 75th annual Cold Spring Harbor Symposium on Quantitative Biology to discuss the organization and function of the cell nucleus. It reviews the latest advances in research into nuclear structure, the organization of the genome within the nucleus, and spatiotemporal coordination of nuclear processes. The topics examined include nuclear domains, chromatin organization, transcription and RNA processing, DNA replication, nuclear reprogramming, and epigenetics. Cancer, premature aging syndromes, and other diseases that may be associated with altered nuclear organization are also covered.
Book Synopsis Bacterial Chromatin by : Remus T. Dame
Download or read book Bacterial Chromatin written by Remus T. Dame and published by Springer Nature. This book was released on with total page 654 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Principles of Nucleic Acid Structure by : Wolfram Saenger
Download or read book Principles of Nucleic Acid Structure written by Wolfram Saenger and published by Springer Science & Business Media. This book was released on 2013-12-01 with total page 574 pages. Available in PDF, EPUB and Kindle. Book excerpt: New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical ther modynamics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the grad uate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases the availability of texts in active research areas should help stimulate the creation of new courses. CHARLES R. CANTOR New York Preface This monograph is based on a review on polynucleotide structures written for a book series in 1976.
Book Synopsis DNA Systems Under Internal and External Forcing by : Megan Clare Engel
Download or read book DNA Systems Under Internal and External Forcing written by Megan Clare Engel and published by Springer Nature. This book was released on 2019-09-17 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt: The interactions of DNA with force are central to manifold fields of inquiry, including the de novo design of DNA nanostructures, the use of DNA to probe the principles of biological self-assembly, and the operation of cellular nanomachines. This work presents a survey of three distinct ways coarse-grained simulations can help characterize these interactions. A non-equilibrium energy landscape reconstruction technique is validated for use with the oxDNA model and a practical framework to guide future applications is established. A novel method for calculating entropic forces in DNA molecules is outlined and contrasted with existing, flawed approaches. Finally, a joint experimental-simulation study of large DNA origami nanostructures under force sheds light on design principles and, through vivid illustrations, their unfolding process. This text provides an accessible and exciting launching point for any student interested in the computational study of DNA mechanics and force interactions.
Book Synopsis Nuclear Architecture and Dynamics by : Christophe Lavelle
Download or read book Nuclear Architecture and Dynamics written by Christophe Lavelle and published by Academic Press. This book was released on 2017-10-27 with total page 620 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nuclear Architecture and Dynamics provides a definitive resource for (bio)physicists and molecular and cellular biologists whose research involves an understanding of the organization of the genome and the mechanisms of its proper reading, maintenance, and replication by the cell. This book brings together the biochemical and physical characteristics of genome organization, providing a relevant framework in which to interpret the control of gene expression and cell differentiation. It includes work from a group of international experts, including biologists, physicists, mathematicians, and bioinformaticians who have come together for a comprehensive presentation of the current developments in the nuclear dynamics and architecture field. The book provides the uninitiated with an entry point to a highly dynamic, but complex issue, and the expert with an opportunity to have a fresh look at the viewpoints advocated by researchers from different disciplines. Highlights the link between the (bio)chemistry and the (bio)physics of chromatin Deciphers the complex interplay between numerous biochemical factors at task in the nucleus and the physical state of chromatin Provides a collective view of the field by a large, diverse group of authors with both physics and biology backgrounds
Book Synopsis Molecular Modeling and Simulation by : Tamar Schlick
Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text
Book Synopsis 2-Oxoglutarate-Dependent Oxygenases by : Christopher J Schofield
Download or read book 2-Oxoglutarate-Dependent Oxygenases written by Christopher J Schofield and published by Royal Society of Chemistry. This book was released on 2015-05-06 with total page 508 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the discovery of the first examples of 2-oxoglutarate-dependent oxygenase-catalysed reactions in the 1960s, a remarkably broad diversity of alternate reactions and substrates has been revealed, and extensive advances have been achieved in our understanding of the structures and catalytic mechanisms. These enzymes are important agrochemical targets and are being pursued as therapeutic targets for a wide range of diseases including cancer and anemia. This book provides a central source of information that summarizes the key features of the essential group of 2-oxoglutarate-dependent dioxygenases and related enzymes. Given the numerous recent advances and biomedical interest in the field, this book aims to unite the latest research for those already working in the field as well as to provide an introduction for those newly approaching the topic, and for those interested in translating the basic science into medicinal and agricultural benefits. The book begins with four broad chapters that highlight critical aspects, including an overview of possible catalytic reactions, structures and mechanisms. The following seventeen chapters focus on carefully selected topics, each written by leading experts in the area. Readers will find explanations of rapidly evolving research, from the chemistry of isopenicillin N synthase to the oxidation mechanism of 5-methylcytosine in DNA by ten-eleven-translocase oxygenases.
Download or read book DNA Topology written by Andrew D. Bates and published by Oxford University Press, USA. This book was released on 2005 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: "A key aspect of DNA is its ability to form a variety of structures, this book explains the origins and importance of such structures"--Provided by publisher.
Book Synopsis The Physics of Cancer by : Caterina A. M. La Porta
Download or read book The Physics of Cancer written by Caterina A. M. La Porta and published by Cambridge University Press. This book was released on 2017-04-20 with total page 187 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent years have witnessed an increasing number of theoretical and experimental contributions to cancer research from different fields of physics, from biomechanics and soft-condensed matter physics to the statistical mechanics of complex systems. Reviewing these contributions and providing a sophisticated overview of the topic, this is the first book devoted to the emerging interdisciplinary field of cancer physics. Systematically integrating approaches from physics and biology, it includes topics such as cancer initiation and progression, metastasis, angiogenesis, cancer stem cells, tumor immunology, cancer cell mechanics and migration. Biological hallmarks of cancer are presented in an intuitive yet comprehensive way, providing graduate-level students and researchers in physics with a thorough introduction to this important subject. The impact of the physical mechanisms of cancer are explained through analytical and computational models, making this an essential reference for cancer biologists interested in cutting-edge quantitative tools and approaches coming from physics.
Book Synopsis Plant Epigenetics by : Nikolaus Rajewsky
Download or read book Plant Epigenetics written by Nikolaus Rajewsky and published by Springer. This book was released on 2017-04-27 with total page 540 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents, in 26 chapters, the status quo in epigenomic profiling. It discusses how functional information can be indirectly inferred and describes the new approaches that promise functional answers, collectively referred to as epigenome editing. It highlights the latest important advances in our understanding of the functions of plant epigenomics and new technologies for the study of epigenomic marks and mechanisms in plants. Topics include the deposition or removal of chromatin modifications and histone variants, the role of epigenetics in development and response to environmental signals, natural variation and ecology, as well as applications for epigenetics in crop improvement. Discussing areas ranging from the complex regulation of stress and heterosis to the precise mechanisms of DNA and histone modifications, it presents breakthroughs in our understanding of complex phenotypic phenomena.
