Statistical Mechanics of Protein Complexed and Condensed DNA PDF Download
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Author: Igor Kulić
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Author: Igor Kulić
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Author: Igor Kulić
Publisher:
ISBN:
Category :
Languages : en
Pages : 149
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Author: Stefan Michael Giovan
Publisher:
ISBN:
Category : DNA repair
Languages : en
Pages : 212
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Book Description
A complex connection exists between the 3 dimensional topological state of DNA in living organisms and biological processes including gene expression, DNA replication, recombination and repair. A significant limitation in developing a detailed, quantitative understanding of this connection is due to a lack of rigorous methods to calculate statistical mechanical properties of DNA molecules with complex topologies, including supercoiling, looping and knotting. This dissertation's main focus is on developing such methods and applying them to realistic DNA and nucleoprotein models. In chapter 2, a method is presented to calculate free energies and J factors of protein mediated DNA loops by normal mode analysis (NMA). This method is similar to calculations performed previously but with several significant advances. We apply the method to the specific case of DNA looping mediated by Cre recombinase protein. J factors calculated by our method are compared to experimental measurements to extract geometric and elastic properties of the Cre-DNA synaptic complex. In particular, the results suggest the existence of a synaptic complex that is more flexible than previously expected and may be explained by a stable intermediate in the reaction pathway that deviates significantly from the planar crystal structure. Calculating free energies of DNA looping is difficult in general, especially when considering intermediate length scales such as plasmid sized DNA which may readily adopt multiple topological states. In chapter 3, a novel method is presented to obtain free energies of semiflexible biopolymers with fixed topologies and arbitrary ratios of contour length L to persistence length P. High accuracy is demonstrated by calculating free energies of specific DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.
Author: Luke Czapla
Publisher:
ISBN:
Category : DNA-protein interactions
Languages : en
Pages : 126
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Book Description
There are many challenges involved in the simulation of DNA. In this work, novel Monte Carlo techniques are developed and applied to understanding the biophysical properties of DNA. A coarse-grained model is applied to feasibly simulate long DNA chains of hundreds to thousands of base pairs, using a reduced base-pair step representation of the DNA. Using this model, a canonical Monte Carlo simulation of DNA is developed to characterize the structure and flexibility of double-helical DNA. By applying a unique algorithm for generating uncorrelated DNA conformations a priori, limitations of the original Metropolis Monte Carlo algorithm are avoided. Furthermore, there is developing experimental evidence that non-specifically associating proteins that induce DNA bending modulate the in-vivo flexibility of DNA. To investigate the effect of these proteins, a grand canonical Monte Carlo simulation technique is developed, extending the model of free DNA to incorporate non-specific protein-DNA interactions. In this technique, DNA chains are simulated with varying numbers of bound proteins. Ubiquitous DNA architectural proteins such as the prokaroytic nucleoid protein HU and the eukaryotic HMG-box proteins are investigated with this technique. By incorporating structural information from the protein-DNA complexes currently available in the Nucleic Acid Database, models of these DNA-binding proteins are constructed and used in this method. The results predict an enhancement of DNA flexibility due to non-specific binding of these proteins, and calculations of the cyclization (ring-closure) properties and force-extension responses of protein-bound DNA chains compared to free DNA chains are presented. In addition, the effects of these proteins on the topological properties of closed circular DNA and on the looping properties of DNA constrained by binding to the Lac repressor protein assembly are characterized in large-scale parallel simulations. Coordination of protein binding on circular and looped DNA and induction of negative supercoiling of DNA by DNA architectural proteins is predicted, with important biological implications for chromosome organization and transcription regulation.
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Category :
Languages : en
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In the thesis work we investigate four problems connected with dynamical processes in condensed medium, using different techniques of equilibrium and non-equilibrium statistical mechanics. Biology is rich in dynamical events ranging from processes involving single molecule [1] to collective phenomena [2]. In cell biology, translocation and transport processes of biological molecules constitute an important class of dynamical phenomena occurring in condensed phase. Examples include protein transport through membrane channels, gene transfer between bacteria, injection of DNA from virus head to the host cell, protein transport thorough the nuclear pores etc. We present a theoretical description of the problem of protein transport across the nuclear pore complex [3]. These nuclear pore complexes (NPCs) [4] are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. The first suggests that the plug is a reversible hydrogel while the other suggests that it is a polymer brush. In the thesis, we propose a model for the transport of a protein through the plug, which is treated as elastic continuum, which is general enough to cover both the models. The protein stretches the plug and creates a local deformation, which together with the protein is referred to as the bubble. The relevant coordinate describing the transport is the center of the bubble. We write down an expression for the energy of the system, which is used to analyze the motion. It shows that the bubble executes a random walk, within the gel. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. Further, on adopting the same kind of free energy for the brush too, one finds that though the energy cost for the entry of the particle is small but the diffusion coefficient is much lower and hence, explanation of the rapid diffusion of the particle across the nuclear pore complex is easier withi.
Author: Gregory A. Voth
Publisher: CRC Press
ISBN: 1420059564
Category : Science
Languages : en
Pages : 492
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Book Description
Exploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems. Assembling some of the most influential, world-renowned researchers in the field, this book covers the latest developments in the coarse-grained molecular dynamics simulation and modeling of condensed phase and biomolecular systems. Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors discuss the minimalist, inversion, and multiscale approaches to coarse-graining, along with the emerging challenges of coarse-graining. They also connect atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA.
Author: Kerson Huang
Publisher: World Scientific Publishing Company Incorporated
ISBN: 9789812561503
Category : Science
Languages : en
Pages : 144
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Book Description
This book introduces an approach to protein folding from the point of view of kinetic theory. There is an abundance of data on protein folding, but few proposals are available on the mechanism driving the process. Here, presented for the first time, are suggestion on possible research directions, as developed by the author in collaboration with C. C. Lin. The first half of this invaluable book contains a concise but relatively complete review of relevant topics in statistical mechanics and kinetic theory. It includes standard topics such as thermodynamics, the Maxwell-Boltzmann distribution, and ensemble theory. Special discussions include the dynamics of phase transitions, and Brownian motion as an illustration of stochastic processes. The second half develops topics in molecular biology and protein structure, with a view to discovering mechanisms underlying protein folding. Attention is focused on the energy flow through the protein in its folded state. A mathematical model, based on the Brownian motion of coupled harmonic oscillators, is worked out in the appendix.
Author: Ivet Bahar
Publisher: Garland Science
ISBN: 1351815016
Category : Science
Languages : en
Pages : 337
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Book Description
Protein Actions: Principles and Modeling is aimed at graduates, advanced undergraduates, and any professional who seeks an introduction to the biological, chemical, and physical properties of proteins. Broadly accessible to biophysicists and biochemists, it will be particularly useful to student and professional structural biologists and molecular biophysicists, bioinformaticians and computational biologists, biological chemists (particularly drug designers) and molecular bioengineers. The book begins by introducing the basic principles of protein structure and function. Some readers will be familiar with aspects of this, but the authors build up a more quantitative approach than their competitors. Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. These chapters illuminate how proteins attain biologically active states and the properties of those states. The book ends with a synopsis the roles of computational biology and bioinformatics in protein science.
Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 2454
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Book Description
Vols. for 1963- include as pt. 2 of the Jan. issue: Medical subject headings.
Author: Jennifer J. McManus
Publisher: Humana
ISBN: 9781493996803
Category : Science
Languages : en
Pages : 266
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Book Description
This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.
