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Molecular Recognition Tools For Chemistry In Living Systems
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Book Synopsis Molecular Recognition Tools for Chemistry in Living Systems by : Anna Kataki Anastasakou
Download or read book Molecular Recognition Tools for Chemistry in Living Systems written by Anna Kataki Anastasakou and published by . This book was released on 2021 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: The introduction of unnatural functionality in biological systems, coupled with detection using bioorthogonal chemical reactions, revolutionized the field of chemical biology by enabling the investigation of biological processes in live cells and simple organisms. However, the translation to complex organisms has led to less-than-optimal results with high background noise due to cross reactivity with activated reagents. This dissertation investigates the utilization of non-covalent chemistry and bioorthogonal host-guest pairs to obtain more efficient labeling of living systems. Complexation between a host and guest is diffusion-limited, hence can be efficient in dilute environments. The cucurbit[n]uril scaffold has been utilized to determine the minimum binding affinity required for efficient bioorthogonal complexation and investigate how guest size and charge affects the introduction of guests as unnatural metabolites. Carboranes, a cucurbit[7]uril guest class that can be removed "on demand" from the host cavity, were found compatible with metabolic glycoengineering and were successfully incorporated on the cell surface. The cucurbit[7]uril-carborane system serves as the first example of bioorthogonal complexation of a metabolically-incorporated guest and answers fundamental questions required for the further development of bioorthogonal host-guest pairs. Finally, work in expanding the properties of unnatural functionality that can be tolerated by biological systems led to the development of fluorescent guest molecules that could be used independently or in conjunction with molecular recognition tools to investigate living systems.Chapter One is a review on the expansion of chemical reporters beyond bioorthogonal chemistry by metabolic incorporation of alternative moieties with novel functions. These chemical reporters expand on our ability to study and manipulate biological processes with non-invasive methods. Chapters Two details the synthetic methodologies for functionalized cucurbit[7]urils. The two main synthetic approaches to obtaining mono-functionalized cucurbit[7]urils were investigated and cucurbit[7]uril-payload conjugates were synthesized that were used in the remaining work on bioorthogonal complexation described in this dissertation. Chapter Three describes the discovery of carboranes as cucurbit[7]uril guests and their derivatization to increase their binding affinity and aqueous solubility. Ortho-carborane is presented as an stimuli-responsive guest that allows recycling cucurbit[7]uril-solid support constructs through multiple payload isolation rounds in cell lysate. Chapter Four introduces bioorthogonal complexation, namely the labeling of cell-surfaces using host-guest chemistry. A variety of cucurbit[7]uril guests were labeled with a cucurbit[7]- uril-fluorescein conjugate to determine the minimum binding affinity required for bioorthogonal complexation. Metabolic incorporation of a cucurbit[7]uril guest is also presented as a sialic acid derivative on the cell surface that can be similarly labeled with cucurbit[7]uril-fluorophore conjugates. Chapters Five explores the functionality of cucurbit[7]uril guests that can be tolerated by the sialic acid biosynthetic pathway along with in vitro and in vivo methods to analyze and determine successful metabolic incorporation. Chapters Six outlines the development of fluorescent guest molecules that can serve as independent fluorophores or in conjuction with bioorthogonal complexation. The mechanism of luminescence is investigated and preliminary in cellulo data is presented that point towards potential applications.
Book Synopsis Computational Tools for Chemical Biology by : Sonsoles Martín-Santamaría
Download or read book Computational Tools for Chemical Biology written by Sonsoles Martín-Santamaría and published by Royal Society of Chemistry. This book was released on 2017-11-01 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research.
Book Synopsis MOLECULAR RECOGNITION: BIOTECHNOLOGY, CHEMICAL ENGINEERING AND MATERIALS APPLICATIONS by : JASON A. MCEVOY
Download or read book MOLECULAR RECOGNITION: BIOTECHNOLOGY, CHEMICAL ENGINEERING AND MATERIALS APPLICATIONS written by JASON A. MCEVOY and published by Lulu.com. This book was released on 2011 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational Tools for Chemical Biology by : Sonsoles Martín-Santamaría
Download or read book Computational Tools for Chemical Biology written by Sonsoles Martín-Santamaría and published by Royal Society of Chemistry. This book was released on 2017-10-25 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: The rapid development of efficient computational tools has allowed researchers to tackle biological problems and to predict, analyse and monitor, at an atomic level, molecular recognition processes. This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research. Chapters from internationally renowned leaders in the field introduce concepts and discuss the impact of technological advances in computer hardware and software in explaining and predicting phenomena involving biomolecules, from small molecules to macromolecular systems. Important topics from the understanding of biomolecules to the modification of their functions are addressed, as well as examples of the application of tools in drug discovery, glycobiology, protein design and molecular recognition. Not only are the cutting-the-edge methods addressed, but also their limitations and possible future development. For anyone wishing to learn how computational chemistry and molecular modelling can provide information not easily accessible through other experimental methods, this book will be a valuable resource. It will be of interest to postgraduates and researchers in the biological and chemical sciences, medicinal and pharmaceutical chemistry, and theoretical chemistry.
Book Synopsis Principles of Molecular Recognition by : A.D. Buckingham
Download or read book Principles of Molecular Recognition written by A.D. Buckingham and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: The importance of molecular recognition in chemistry and biology is reflected in a recent upsurge in relevant research, promoted in particular by high-profile initiatives in this area in Europe, the USA and Japan. Although molecular recognition is necessarily microscopic in origin, its consequences are de facto macroscopic. Accordingly, a text that starts with intermolecular interactions between simple molecules and builds to a discussion of molecular recognition involving larger scale systems is timely. This book was planned with such a development in mind. The book begins with an elementary but rigorous account of the various types of forces between molecules. Chapter 2 is concerned with the hydrogen bond between pairs of simple molecules in the gas phase, with particular reference to the preferred relative orientation of the pair and the ease with which this can be distorted. This microscopic view continues in chapter 3 wherein the nature of interactions between solute molecules and solvents or between two or more solutes is examined from the experimental standpoint, with various types of spectroscopy providing the probe of the nature of the interactions. Molecular recognition is central to the catalysis of chemical reactions, especially when bonds are to be broken and formed under the severe con straint that a specific configuration is to result, as in the production of enan tiotopically pure compounds. This important topic is considered in chapter 4.
Book Synopsis Molecular Recognition Mechanisms by : Michel Delaage
Download or read book Molecular Recognition Mechanisms written by Michel Delaage and published by Wiley-VCH. This book was released on 1991 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Recognition in Chemical and Biological Systems by : Margaret Mary Harding
Download or read book Molecular Recognition in Chemical and Biological Systems written by Margaret Mary Harding and published by . This book was released on 2001 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Cellular and Biomolecular Recognition by : Raz Jelinek
Download or read book Cellular and Biomolecular Recognition written by Raz Jelinek and published by John Wiley & Sons. This book was released on 2009-07-10 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: With its exploration of the scientific and technological characteristics of systems exploiting molecular recognition between synthetic materials, such as polymers and nanoparticles, and biological entities, this is a truly multidisciplinary book bridging chemistry, life sciences, pharmacology and medicine. The authors introduce innovative biomimetic chemical assemblies which constitute platforms for recruitment of cellular components or biological molecules, while also focusing on physical, chemical, and biological aspects of biomolecular recognition. The diverse applications covered include biosensors, cell adhesion, synthetic receptors, cell patterning, bioactive nanoparticles, and drug design.
Book Synopsis Protein Surface Recognition by : Ernest Giralt
Download or read book Protein Surface Recognition written by Ernest Giralt and published by John Wiley & Sons. This book was released on 2011-07-07 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: A new perspective on the design of molecular therapeutics is emerging. This new strategy emphasizes the rational complementation of functionality along extended patches of a protein surface with the aim of inhibiting protein/protein interactions. The successful development of compounds able to inhibit these interactions offers a unique chance to selectively intervene in a large number of key cellular processes related to human disease. Protein Surface Recognition presents a detailed treatment of this strategy, with topics including: an extended survey of protein-protein interactions that are key players in human disease and biology and the potential for therapeutics derived from this new perspective the fundamental physical issues that surround protein-protein interactions that must be considered when designing ligands for protein surfaces examples of protein surface-small molecule interactions, including treatments of protein-natural product interactions, protein-interface peptides, and rational approaches to protein surface recognition from model to biological systems a survey of techniques that will be integral to the discovery of new small molecule protein surface binders, from high throughput synthesis and screening techniques to in silico and in vitro methods for the discovery of novel protein ligands. Protein Surface Recognition provides an intellectual “tool-kit” for investigators in medicinal and bioorganic chemistry looking to exploit this emerging paradigm in drug discovery.
Book Synopsis Beyond the Molecular Frontier by : National Research Council
Download or read book Beyond the Molecular Frontier written by National Research Council and published by National Academies Press. This book was released on 2003-03-19 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemistry and chemical engineering have changed significantly in the last decade. They have broadened their scopeâ€"into biology, nanotechnology, materials science, computation, and advanced methods of process systems engineering and controlâ€"so much that the programs in most chemistry and chemical engineering departments now barely resemble the classical notion of chemistry. Beyond the Molecular Frontier brings together research, discovery, and invention across the entire spectrum of the chemical sciencesâ€"from fundamental, molecular-level chemistry to large-scale chemical processing technology. This reflects the way the field has evolved, the synergy at universities between research and education in chemistry and chemical engineering, and the way chemists and chemical engineers work together in industry. The astonishing developments in science and engineering during the 20th century have made it possible to dream of new goals that might previously have been considered unthinkable. This book identifies the key opportunities and challenges for the chemical sciences, from basic research to societal needs and from terrorism defense to environmental protection, and it looks at the ways in which chemists and chemical engineers can work together to contribute to an improved future.
Book Synopsis Chemical Tools for Imaging, Manipulating, and Tracking Biological Systems: Diverse Chemical, Optical and Bioorthogonal Methods by :
Download or read book Chemical Tools for Imaging, Manipulating, and Tracking Biological Systems: Diverse Chemical, Optical and Bioorthogonal Methods written by and published by Academic Press. This book was released on 2020-07-24 with total page 526 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Tools for Imaging, Manipulating, and Tracking Biological Systems: Diverse Chemical, Optical and Bioorthogonal Methods, Volume 641 in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Chapters in this new release include caged cyclopropanes with improved tetrazine ligation kinetics, an analysis of metabolically labeled inositol phosphate messengers by NMR, cell-permeant caged inositol pyrophosphates for probing ß-cells, imaging phospholipase D activity with clickable alcohols via transphosphatidylation, fluorescent biorthogonal labeling of class B GPCRs in live cells, near-infrared photoactivatable nitric oxide donors with integrated photoacoustic monitoring, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Includes the latest information on retinoid signaling pathways
Book Synopsis Physical Biology: From Atoms To Medicine by : Ahmed H Zewail
Download or read book Physical Biology: From Atoms To Medicine written by Ahmed H Zewail and published by World Scientific. This book was released on 2008-05-06 with total page 582 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is an avant-garde book edited by Nobel Laureate Ahmed Zewail with contributions from eminent scientists including four Nobel prize winners. The perspectives of these world leaders in physics, chemistry, and biology define potential new frontiers at the interface of disciplines and including physical, systems, and synthetic biology.This book brings about the confluence of concepts and tools, and that of different disciplines, to address significant problems of our time: visualization; theory and computation for complexity; macromolecular function, protein folding and misfolding; and systems integration from cells to consciousness. The scope of tools is wide-ranging, spanning imaging, crystallography, microfluidics, single-molecule spectroscopy, and synthetic probe targeting. Concepts such as dynamic self-assembly, molecular recognition, non-canonical amino acids, and others are covered in various chapters as they are cornerstones in building the trilogy description of behavior-structure, dynamics, and function.The volume is uniquely structured to provide overviews with historical perspectives on the evolution of ideas and on the future of physical biology and biological complexity, from atoms to medicine./a
Book Synopsis Molecular Recognition and Inclusion by : A.W. Coleman
Download or read book Molecular Recognition and Inclusion written by A.W. Coleman and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents articles on the developing field of molecular interactions, molecular recognition, crystal engineering, and structural determination of complex molecular systems. The approaches described are interdisciplinary in nature, reflecting the concept of the ISMRI series of symposia.
Book Synopsis Research at the Intersection of the Physical and Life Sciences by : National Research Council
Download or read book Research at the Intersection of the Physical and Life Sciences written by National Research Council and published by National Academies Press. This book was released on 2010-03-25 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt: Traditionally, the natural sciences have been divided into two branches: the biological sciences and the physical sciences. Today, an increasing number of scientists are addressing problems lying at the intersection of the two. These problems are most often biological in nature, but examining them through the lens of the physical sciences can yield exciting results and opportunities. For example, one area producing effective cross-discipline research opportunities centers on the dynamics of systems. Equilibrium, multistability, and stochastic behavior-concepts familiar to physicists and chemists-are now being used to tackle issues associated with living systems such as adaptation, feedback, and emergent behavior. Research at the Intersection of the Physical and Life Sciences discusses how some of the most important scientific and societal challenges can be addressed, at least in part, by collaborative research that lies at the intersection of traditional disciplines, including biology, chemistry, and physics. This book describes how some of the mysteries of the biological world are being addressed using tools and techniques developed in the physical sciences, and identifies five areas of potentially transformative research. Work in these areas would have significant impact in both research and society at large by expanding our understanding of the physical world and by revealing new opportunities for advancing public health, technology, and stewardship of the environment. This book recommends several ways to accelerate such cross-discipline research. Many of these recommendations are directed toward those administering the faculties and resources of our great research institutions-and the stewards of our research funders, making this book an excellent resource for academic and research institutions, scientists, universities, and federal and private funding agencies.
Book Synopsis Molecular Recognition Modeling by : Wanli You
Download or read book Molecular Recognition Modeling written by Wanli You and published by . This book was released on 2017 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Recent Trends in Molecular Recognition by : F. Diederich
Download or read book Recent Trends in Molecular Recognition written by F. Diederich and published by Springer. This book was released on 1998-12-03 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: Reasoning in terms of molecular recognition may be traced back to Emil Fischer, who practiced the art of chemistry at Humboldt University in Prussian Berlin a century ago. Today, it is clearly recognized that molecular recognition impacts and determines all life processes. It has become a key research field in both chemistry and biology and the emerging interface of what now is being called "chemical biology". The technological advances derived from this knowledge are particularly important, diverse, and directly evident in the pharmaceutical industry. Under the auspices of the Ernst Schering Research Foundation, a workshop held in Berlin in February 1998 addressed novel basic developments of potential relevance to drug research efforts. A balance of timely research topics in molecular recognition is presented in the lectures delivered by a multidisciplinary international panel of renowned scholars and documented in this volume.
Book Synopsis An Introduction to Molecular Recognition Approach. Tool for Environmental Analysis by : Bilal Bhat
Download or read book An Introduction to Molecular Recognition Approach. Tool for Environmental Analysis written by Bilal Bhat and published by . This book was released on 2018-12-20 with total page 20 pages. Available in PDF, EPUB and Kindle. Book excerpt: Document from the year 2018 in the subject Chemistry - Analytical Chemistry, grade: Ist, course: Chemical Sciences, language: English, abstract: Owing to the boom of Industrialization and modernization, diverse chemical entities have found entrance into various environmental components. Thus the continous monitoring of environment has been a crucial issue to the community. In this regard, development of novel technologies have urged a surge in the recent past. Among the various approaches proposed by the researchers, supramolecular chemistry has came up with intelligent state of art molecules know as " Receptors". These can be organic or inrganic moities which secreen the diverse chemical environments through visual display. They possess immense potential to overcome the diffculties associated with exisiting bulky and tedious strategies for environmental monitoring. In this book chapter, we have tried to present an introduction to this molecular approach for sensing of various chemical species in the form of caion and anions. The basic classification of the molecular receptor approach has been introduced. This has been further exaplained via the mechanism of intraction between molecule and analyte durring the course of sensng in diverse environmental matrices.
