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Book Synopsis On the Conformational Dynamics of DNA by : Ning Ma
Download or read book On the Conformational Dynamics of DNA written by Ning Ma and published by . This book was released on 2017 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: The main focus of my dissertation is on the conformational motion of DNA, studied by applying tools from the computational chemistry field. In addition, studies of relative α- and 310 helical stabilities in peptides/mini-proteins, and a molecular flooding study of the retinoid X-receptor as part of a continuing drug design effort are presented. In molecular biology, it has been well known that sequence determines structure, and structure controls function. For proteins or DNA to work properly, the correct configuration is required. Mutations may alter the structure, which can cause malfunction. Non-mutational effects, such as a change in environment may also cause a configurational change and in turn change the functionality of the protein or DNA. Many experimental technics have been developed to investigate the structural or configurational aspects of biological systems, and molecular dynamics simulation has been proven to be a useful complementary tool to gain insights into this problem due to its ability to explore the dynamics and energetics of biomolecular processes at high spatial and time resolution. Molecular dynamics simulations are constrained by the available computational power, but several computational techniques have been developed to reduce computational costs. Also, development of hardware has helped the issue. Years of hard work on force field parameter optimization built a solid foundation for molecular dynamics simulations, so that the computational model can satisfactory describe many biochemical systems in detail. Techniques such as umbrella ix sampling and reweighting methods have allowed researchers to construct free energy landscapes to reveal the relative stabilities of each major configurational state and the free energy barriers between configurations from relatively short simulations, a process which would otherwise require many microseconds of unbiased simulations.
Book Synopsis A Study of DNA Conformational Dynamics Using Single-molecule Fluorescence Resonance Energy Transfer by : Mark Ian Wallace
Download or read book A Study of DNA Conformational Dynamics Using Single-molecule Fluorescence Resonance Energy Transfer written by Mark Ian Wallace and published by . This book was released on 2001 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Conformational Dynamics by : Ke-li Han
Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Book Synopsis Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition by : Yogambigai Velmurugu
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.
Book Synopsis Biophysics of DNA by : Alexander Vologodskii
Download or read book Biophysics of DNA written by Alexander Vologodskii and published by Cambridge University Press. This book was released on 2015-03-12 with total page 279 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book surveys the last sixty years of research in the rapidly advancing field of DNA biophysics, addressing key questions and facilitating further research.
Book Synopsis Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding by :
Download or read book Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding written by and published by . This book was released on 2008 with total page 33 pages. Available in PDF, EPUB and Kindle. Book excerpt: While the Watson-Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By rising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA. Based on the Poland-Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation bubbles and selectively single stranded DNA binding proteins.
Book Synopsis Multi-disciplinary Investigation of the Kinetics and Protein Conformational Dynamics of DNA Replication and Oxidative DNA Damage Bypass and Repair by : Brian Andrew Maxwell
Download or read book Multi-disciplinary Investigation of the Kinetics and Protein Conformational Dynamics of DNA Replication and Oxidative DNA Damage Bypass and Repair written by Brian Andrew Maxwell and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: My working hypothesize is that, in order to regulate polymerase switching and DNA damage repair, DNA damage sites can alter various properties of DNA polymerases and the enzymes involved in BER including how they bind to DNA, the rate at which they perform their catalytic functions and how they change their structures during the course of the reaction. In order to test this hypothesis I have utilized rapid mixing techniques to investigate how the presence of a DNA lesion will affect the rates of DNA copying for both replicative and specialized DNA polymerases. By utilizing fluorescence spectroscopy I have investigated how the presence of DNA damage affects the structural changes that the enzymes undergo when binding to DNA as well as when interacting with other substrates and protein cofactors. These fluorescence based studies make use of Forster Resonance Energy Trans (FRET), which serves as a "molecular ruler" to monitor the change in distance between two fluorescent markers which can be placed at specific locations on the enzymes and/or DNA. Finally, I have investigated the interactions between the enzymes and the DNA or between two enzymes on the level of individual molecules using a state-of-the-art single molecule FRET microscopy system that I designed and assembled. Collectively, the results from this research project have provided novel insight into the conformational dynamics and kinetics of the molecular interactions involved in DNA replication and DNA damage repair in the BER pathway.
Download or read book CRISPR written by Rodolphe Barrangou and published by John Wiley & Sons. This book was released on 2022-09-14 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: “An excellent compendium of all things CRISPR from some of the leading minds in the field. With thorough coverage from every angle and beautifully detailed illustrations, this book is not to be missed!” Jennifer A. Doudna, Professor of Chemistry, Biochemistry & Molecular Biology, UC Berkeley; Founder, Innovative Genomics Institute; Nobel Laureate and coinventor of CRISPR technology “This journey through CRISPR biology and several of its breakthrough applications offers an exciting glimpse into one of the most beautiful and compelling fields in the life sciences.” David R. Liu, Director of the Merkin Institute at the Broad Institute of MIT and Harvard; Professor of Chemistry and Chemical Biology at Harvard University; coinventor of base editing and prime editing “A must read! The CRISPR topics, written by world-leading experts, span from the fascinating mechanistic underpinnings to the ingenious applications. One can read from start to finish or pick and choose themes. Either way, the book delivers utterly enjoyable learning!” Bonnie Bassler, Squibb Professor and Chair, Princeton University Department of Molecular Biology; Howard Hughes Medical Institute Investigator CRISPR-Cas systems have revolutionized the science of gene editing and their possible applications continue to expand, from basic research to potentially groundbreaking medical and commercial uses. Led by a distinguished team of editors, CRISPR: Biology and Applications explores the subject matter needed to delve into this fascinating area. Topics covered include: Classification and molecular mechanisms of CRISPR-Cas systems CRISPR-Cas evolution, regulation, expression, and function Uses for gene editing and modulation of gene expression CRISPR-based antimicrobials and phage resistance for medical and industrial purposes Written by internationally renowned authors, CRISPR: Biology and Applications serves as both an introductory guide for those new to the field and an authoritative reference for seasoned researchers whose work touches this evolving and headline- making science.
Book Synopsis Single-molecule Spectroscopy Studies of Protein Conformational Dynamics in DNA Damage Recognition and Cell Signaling by : Sunidhi Jaiswal
Download or read book Single-molecule Spectroscopy Studies of Protein Conformational Dynamics in DNA Damage Recognition and Cell Signaling written by Sunidhi Jaiswal and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-molecule fluorescence spectroscopy has been developed as a powerful technique that provides details of protein-protein and protein-DNA interactions, enzyme reactions, and conformational dynamics. It is highly informative to study protein's conformational dynamics during their activity or under the enzymatic condition to understand their function. The real-time monitoring of the enzyme's active site conformational dynamics and simultaneously activity is informative towards understanding the mechanism of action. Studying how conformational fluctuation dynamics play role in protein or enzyme activity can shed light on the field of enzymology. Particularly in this dissertation, we have employed FoÌrster Resonance Energy Transfer (FRET) as a powerful tool to study the conformational dynamics of Calmodulin (CaM) during its interaction with an autoinhibitory domain (C28W peptide) of the Plasma Membrane Calcium ATPase (PMCA). FRET between donor dye-labeled N-domain of the calmodulin interacting with acceptor dye-labeled peptide reports the real-time conformational dynamics of this interaction which is essential for PMCA activation. Interestingly, by using a unique statistical method, the results provide a mechanistic understanding of CaM signaling interaction and activation of the Ca-ATPase through multiple-state binding to the C28W. The new single-molecule spectroscopic analyses demonstrated in this work can be applied for broad studies of protein functional conformation fluctuation and protein-protein interaction dynamics. In another study, the conformational dynamics of recognition proteins are studied to understand the mechanism of identification of DNA damage by two recognition proteins, Replication Protein A (RPA) and Xeroderma Pigmentosum Protein A (XPA). We use single-molecule fluorescence fluctuation measurements of a dye, labeled at a damaged position on DNA, to understand the interaction of the damage site with RPA14 and XPA. Our results suggest that interactive conformational dynamics of RPA14 with damaged DNA are inhomogeneous due to its low affinity for DNA, whereas binding of XPA with the already formed DNA- RPA14 complex may increase the specificity of damage recognition by controlling the conformational fluctuation dynamics of the complex. Further, we studied the activation of calmodulin by applying compressive force using the AFM technique. Significantly, we found that the picoNewton level compressive force can turn a calcium-free CaM molecule into an active binding form just like the calcium-activated CaM.
Book Synopsis High Pressure Bioscience by : Kazuyuki Akasaka
Download or read book High Pressure Bioscience written by Kazuyuki Akasaka and published by Springer. This book was released on 2015-07-14 with total page 722 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume covers both the basic concepts and theory of bio-macromolecules under pressure and the various frontiers in high-pressure bioscience and biotechnology. A century has passed since Bridgman discovered the irreversible coagulation of egg white by applying pressure at 700 atmospheres in 1914. Today we are able to monitor pressure-dependent changes in protein structure as a reversible process even at atomic scale with modern spectroscopic techniques. We can study the fluctuating reality of protein structures as designed by nature, which is the basis for all dynamism of life on earth. We are currently facing a new era of high-pressure bioscience, in which pressure is no longer an “odd” or “foreign” variable to life, but rather an integrated part of it. Pressure is used as a crucial variable for disclosing the secrets of nature and as a powerful new tool for enhancing certain reactions in bio-macromolecules and even in living cells for our practical and industrial needs. A dramatic advancement of high-pressure bioscience both in the basic and the applied sciences is thus anticipated in near future, for which sharing the current advanced knowledge on structure and dynamics of bio-macromolecules under pressure among researchers in both fields is crucial. This book serves as a valuable resource not only for those working directly in a pressure-related field, but also for those working in many other fields of the biosciences. Particularly, the basic part of it is intended to serve as a classical text book on high-pressure bioscience to a wide audience including students and researchers in both basic and applied fields in years to come. Readers can focus on topics of immediate interest first, but may wish to go over other chapters if interest arises in a later occasion.
Book Synopsis Biomolecule Conformational Dynamics Studies Using Two-beam Fluorescence Fluctuation Spectroscopy by : Jaemyeong Jung
Download or read book Biomolecule Conformational Dynamics Studies Using Two-beam Fluorescence Fluctuation Spectroscopy written by Jaemyeong Jung and published by . This book was released on 2005 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis In Vitro, in Silico and in Vivo Studies of the Structure and Conformational Dynamics of DNA Polymerase I. by : Marko Sustarsic
Download or read book In Vitro, in Silico and in Vivo Studies of the Structure and Conformational Dynamics of DNA Polymerase I. written by Marko Sustarsic and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods by :
Download or read book Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods written by and published by Academic Press. This book was released on 2016-10-28 with total page 618 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-Molecule Enzymology, Part A, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in single-molecule enzymology, and includes sections on such topics as force-based and hybrid approaches, fluorescence, high-throughput sm enzymology, nanopores, and tethered particle motion. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in single-molecule enzymology Contains sections on such topics as force-based and hybrid approaches, fluorescence, high-throughput sm enzymology, nanopores, and tethered particle motion
Book Synopsis Binding Site Structure and Conformational Dynamics in the Sequence-Specific Recognition of SsDNA by an Autoantibody by : Melissa J. Bobeck
Download or read book Binding Site Structure and Conformational Dynamics in the Sequence-Specific Recognition of SsDNA by an Autoantibody written by Melissa J. Bobeck and published by . This book was released on 2006 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Dna Solution Structure Dynamics by : Manish Biyani
Download or read book Dna Solution Structure Dynamics written by Manish Biyani and published by LAP Lambert Academic Publishing. This book was released on 2011-05 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: Studies on the solution structure dynamics of RNA/DNA are becoming crucially important. The phenomena of SSCP (single-strand conformation polymorphism), microRNA dynamics in a cell, and others can be related to the conformational changes of single-stranded (ss) RNAs/DNAs in solution. These molecule, which no longer forms a helix, can adopt many different conformations in solution. What are typical conformations of these molecules and what factors govern their conformational space? To answer these important biological questions we need to explore the three broad areas: 1) How does the shape of DNA and its surroundings mutually influence each other? Can we determine their existing relationship? 2) How is the DNA sequence related to its structure? Can we determine the structurally important residues based on the DNA sequence? 3) How is the DNA sequence related to its function? Can we determine the functionally important residues based on the DNA sequence? These and similar questions which require the knowledge of accurate molecular conformations have been studied in this book in an understandable fashion and in order to gain insight into the structure dynamics of DNA in solution.
Book Synopsis Time-resolved NMR-spectroscopic Studies of Conformational Dynamics in DNA G-quadruplexes by : J. Tassilo Grün
Download or read book Time-resolved NMR-spectroscopic Studies of Conformational Dynamics in DNA G-quadruplexes written by J. Tassilo Grün and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Conformational Dynamics Control Catalysis in Disparate Systems by : Jeremy Wayne Setser
Download or read book Conformational Dynamics Control Catalysis in Disparate Systems written by Jeremy Wayne Setser and published by . This book was released on 2014 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical reactions allow biological systems to function. The majority of these biochemical reactions occur due to the work of protein catalysts known as enzymes. These biocatalysts are often thought of as pre-formed, static 'locks' that bind, and subsequently transform, their substrate molecule 'keys'. However, scientists are increasingly finding that dynamic movements of enzymes are a crucial aspect of catalysis. One such example of a system that relies on conformational flexibility is the human DNA repair protein alkyladenine DNA glycosylase (AAG). To efficiently repair DNA, AAG must search the million-fold excess of unmodified DNA bases to find a handful of DNA lesions. Such a search can be facilitated by the ability of glycosylases, like AAG, to interact with DNA using two affinities: a lower-affinity interaction in a searching process, and a higher-affinity interaction for catalytic repair. We have captured crystallographic snapshots of AAG bound to DNA in both high- and lower-affinity states. These depictions reveal several significant and unexpected protein structural rearrangements, providing molecular insight into the DNA-searching process adopted by AAG. By combining these new insights with existing biochemical and structural data, we are able to relate AAG to the big picture question of how DNA binding proteins find their binding sites in the vast expanse of the genome. In another study, a member of a biosynthetic pathway for antibiotic natural products, called kutznerides, was shown to be dependent on conformational changes. The enzyme in question, KtzI, uses a bound flavin cofactor, reducing equivalents from NADPH, and molecular oxygen to install a hydroxyl group on the side-chain nitrogen of the amino acid L-ornithine, which is subsequently incorporated into the kutzneride scaffold. KtzI was structurally characterized after being subjected to various chemical and environmental factors, capturing the enzyme in several states along its catalytic trajectory. These states suggest that a novel conformational change of both the protein backbone and the flavin moiety must take place in order to complete the enzymatic cycle of KtzI. This drastic rearrangement was also shown to be chemically interchangeable in the protein crystal, suggesting that these dynamic motions are catalytically relevant.
