Statistical Mechanical Modeling of Protein-DNA Binding PDF Download
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Author: George Locke
Publisher:
ISBN:
Category : DNA-binding proteins
Languages : en
Pages : 136
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Book Description
Author: George Locke
Publisher:
ISBN:
Category : DNA-binding proteins
Languages : en
Pages : 136
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Book Description
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.
Author: Matthias Siebert
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
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: Yakov M Tseytlin
Publisher: Academic Press
ISBN: 0128020369
Category : Science
Languages : en
Pages : 318
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Book Description
Advanced Mechanical Models of DNA Elasticity includes coverage on 17 different DNA models and the role of elasticity in biological functions with extensive references. The novel advanced helicoidal model described reflects the direct connection between the molecule helix structure and its specific properties, including nonlinear features and transitions. It provides an introduction to the state of the field of DNA mechanics, known and widely used models with their short analysis, as well as coverage on experimental methods and data, the influence of electrical, magnetic, ionic conditions on the persistence length, and dynamics with viscosity influence. It then addresses the need to understand the nature of the non-linear overstretching transition of DNA under force and why DNA has a negative twist-stretch coupling. Includes coverage of 17 contemporary models of DNA mechanics with analysis Provides comparison of DNA and RNA mechanical features Covers advances in experimental techniques including AFM, X-ray, and optical tweezers Contains extensive references for further reading
Author: Harald Seitz
Publisher: Springer Science & Business Media
ISBN: 3540481478
Category : Medical
Languages : en
Pages : 212
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Book Description
With contributions by numerous experts
Author: Gary Stormo
Publisher:
ISBN: 9781936113491
Category : Science
Languages : en
Pages : 198
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Book Description
One of the foundations of molecular biology is how the interactions of proteins with DNA control many aspects of gene expression. Since the mid-20th century discoveries of the lac repressor and operator and the competition between the cI and cro proteins for the same segment of DNA, we have learned an enormous amount about the interactions of proteins with DNA and their control of fundamental processes in the cell. Introduction to Protein-DNA Interactions: Structure, Thermodynamics, and Bioinformatics describes what we know about protein-DNA interactions from the complementary perspectives of molecular and structural biology and bioinformatics and how each perspective informs the others. A particular emphasis is on how insights from experimental work can be translated into specific computational approaches to create unified view of the field and a fuller understanding of protein-DNA interactions.
Author: Nora Dawn Laiken
Publisher:
ISBN:
Category :
Languages : en
Pages : 132
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Book Description
Author: Hamid Bolouri
Publisher: World Scientific Publishing Company
ISBN: 1848168187
Category : Science
Languages : en
Pages : 341
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Book Description
This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Mathematical jargon is avoided and explanations are given in intuitive terms. In cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are provided for use in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal for self-learning and also as the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, or systems biology./a
Author: Kerson Huang
Publisher: World Scientific
ISBN: 9812561439
Category : Science
Languages : en
Pages : 159
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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.
