Molecular Recognition Mechanisms in DNA Binding Protein Families, Using Molecular Modelling Techniques PDF Download
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Author: Richard James Gamblin
Publisher:
ISBN:
Category :
Languages : en
Pages : 300
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Author: Richard James Gamblin
Publisher:
ISBN:
Category :
Languages : en
Pages : 300
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Author: Bruce Alberts
Publisher:
ISBN: 9780815332183
Category : Cytology
Languages : en
Pages : 0
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Author: Wanli You
Publisher:
ISBN: 9780355471953
Category : Cheminformatics
Languages : en
Pages : 262
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Book Description
Molecular recognition is fundamentally important in biological chemistry. Nowadays, with the rapid development of computational technology and algorithm, molecular modeling has become a powerful tool in studying molecular recognition, such as exploring molecular interactions and understanding biological dynamic processes, making significant contributions to modern biology and drug discovery. The state-of-the-art techniques of computational chemistry and molecular modeling can be applied to study a wide range of chemical and biological systems of interest. This enables us to study structural details at the atomic level and obtain chemical/biological information which is not available by experimental measurements. This dissertation project focused on modeling the recognition mechanisms of biomolecules and their conjugated ligands. Multiple computational techniques, such as molecular dynamics simulation, enhanced sampling methods and free energy calculation were applied. The model systems included signaling domains (BRCT domain), kinase (p38 kinase), enzyme system (TRPS) and small biomolecular system (cyclodextrin). The details of protein-ligand interactions, including both enthalpic and entropic contribution within protein domain-phosphopeptide systems were investigated, based on which new inhibitors were proposed. Several enhanced sampling methods like accelerated molecular dynamics simulation, pathway search guided by internal motions (PSIM) and umbrella sampling, were applied to explore the dissociation pathway of kinase-ligand systems and the motions of kinase during dissociation process were studied both thermodynamically and kinetically, protein conformational rearrangement was found to differentiate slow and fast unbinding inhibitors, casting light on high efficacy inhibitor design. Furthermore, using full structural molecular modeling, we explored how the position of a single proton can change the overall protein dynamics and further activate or inactivate enzyme catalysis, elucidating the catalytic mechanism of TRPS. In addition, we performed systematically evaluation to the performance of umbrella sampling, investigated the influence of subtle changes in the dissociation pathways and conformational sampling methods that provide the initial conformations, paving way for future improvement of umbrella sampling. This project studies the details of receptor-ligand interaction and provides a more complete picture of molecular recognition.
Author: Kiyoshi Nagai
Publisher: Oxford University Press, USA
ISBN:
Category : Medical
Languages : en
Pages : 302
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Book Description
The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Author: Phoebe A. Rice
Publisher: Royal Society of Chemistry
ISBN: 0854042725
Category : Science
Languages : en
Pages : 417
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Book Description
This book provides both in-depth background and up-to-date information in this area. The chapters are organized by general themes and principles, written by experts who illustrate topics with current findings. Topics covered include: - the role of ions and hydration in protein-nucleic acid interactions - transcription factors and combinatorial specificity - indirect readout of DNA sequence - single-stranded nucleic acid binding proteins - nucleic acid junctions and proteins, - RNA protein recognition - recognition of DNA damage. It will be a key reference for both advanced students and established scientists wishing to broaden their horizons.
Author: Hisato Kondoh
Publisher: Academic Press
ISBN: 0128004207
Category : Science
Languages : en
Pages : 345
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Book Description
Sox2: Biology and Role in Development and Disease offers a thorough discussion of the important role of Sox2 in cellular and developmental processes, aimed at facilitating greater understanding of how Sox2 functions across different disciplines. The book discusses the basic biology of Sox2 to help establish the critical foundational knowledge necessary for deeper molecular and functional analysis. The book also provides insight into how the Sox2 transcription factor plays a key role in pluripotency induction, maintenance, and development. Helpful as a tool to organize new research projects, the book assists with preparing lessons, seminars, and thesis or research papers, thereby circumventing the need to spend hours searching through journal databases. A single source for the basic biology of Sox2, Sox2: Biology and Its Role in Development and Disease provides information on networks, gene regulation, and regulatory function in a number of cell types and tissues types. Discusses the important role of Sox2 in cellular and developmental processes Facilitates a greater understanding of how Sox2 functions across different disciplines Assists in identifying, circumventing and modifying the dynamics of Sox2 in cell types Provides greater understanding of the structure of Sox2 and its gene networks Identifies aspects of phenotypic spectrum uncovered following greater understanding of Sox2 during development
Author: Mark A. Williams
Publisher: Humana
ISBN: 9781493958733
Category : Science
Languages : en
Pages : 0
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Book Description
Proteins are the cell’s workers, their messengers and overseers. In these roles, proteins specifically bind small molecules, nucleic acid and other protein partners. Cellular systems are closely regulated and biologically significant changes in populations of particular protein complexes correspond to very small variations of their thermodynamics or kinetics of reaction. Interfering with the interactions of proteins is the dominant strategy in the development of new pharmaceuticals. Protein Ligand Interactions: Methods and Applications, Second Edition provides a complete introduction to common and emerging procedures for characterizing the interactions of individual proteins. From the initial discovery of natural substrates or potential drug leads, to the detailed quantitative understanding of the mechanism of interaction, all stages of the research process are covered with a focus on those techniques that are, or are anticipated to become, widely accessible and performable with mainstream commercial instrumentation. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Protein Ligand Interactions: Methods and Applications, Second Edition serves as an ideal guide for researchers new to the field of biophysical characterization of protein interactions – whether they are beginning graduate students or experts in allied areas of molecular cell biology, microbiology, pharmacology, medicinal chemistry or structural biology.
Author: Christopher J Schofield
Publisher: Royal Society of Chemistry
ISBN: 1849739501
Category : Science
Languages : en
Pages : 508
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Book Description
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.
Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1828
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Book Description
Author: Tamar Schlick
Publisher:
ISBN:
Category : Biomolecules
Languages : en
Pages : 0
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Book Description
This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts.
