TLR4 is one of the most important innate immunity receptors, its function mainly consisting in the activation of inflammatory pathways in response to stimulation by Pathogen-Associated Molecular Patterns (PAMPs) and Damage Associated Molecular Pattern molecules (DAMPs). This volume critically reviews the different types of TLR4 activators and inhibitors, discusses the role of molecular aggregates in agonism/antagonism as well as the pivotal role of the CD14 receptor in the modulation of TLR4 signal and the molecular details and actors of the intracellular cascade. The book presents the role of TLR4 in several pathologies, such as sepsis and septic shock caused by receptor activation by gram-negative bacterial lipopolysaccharide (LPS), in neurodegenerative and neurological diseases such as Parkinson and Alzheimer's diseases, and Amyotrophic Lateral Sclerosis (ALS). It reviews the role of TLR4 in neural stem cell-mediated neurogenesis and neuroinflammation and in Human Induced Pluripotent Stem Cells and Cerebral Organoids and discusses the emerging role of micro-RNA (miRNA) regulation by TLR4.

This new edition continues to illustrate the power of biological data in knowledge discovery. It describes biological data types and representations with examples for creating a workflow in bioinformation discovery. The concepts in knowledge discovery from data are illustrated using line diagrams. The principles and concepts in knowledge discovery are used for the development of prediction models for simulations of biological reactions and events. Advanced topics in molecular evolution and cellular & molecular biology are addressed using bioinformation gleaned through discovery. Each chapter contains approximately 10 exercises for practice. This will help students to expand their problem solving skills in Bioinformation Discovery. In this new edition, there are three new chapters covering single nucleotide polymorphism, genes, proteins and disease, and protein functions driven by surface electrostatics.

Plant signalling has emerged as an integrated field which has become indispensable in recent times to study any biological process. Over the last decade, an enormous amount of information has been generated in this field and the advances in information technology gave birth to bioinformatics which has helped greatly in managing the galaxy of information. It is now possible to view the different information s in a systems biology approach which has unravelled the association/ new processes and thus helped us enormously in understanding of the biological processes. The present book is an attempt at understanding the plant signalling processes with different perspectives. Even though the plants are sessile but there exists a tremendous interconnected network of perception at morphological, physiological and molecular levels. The impact of the surrounding environment in terms of abiotic and biotic stresses is significant in terms of its survival, adaptation and productivity for the human welfare. The plants possess a wide array of processes at the organ, tissue and cellular levels which are governed by a plethora of molecules. The molecules govern individual processes and these exists a cross talk between them to form a complex network of processes. The book tries to envision how different processes are operating at different points in the life cycle of the plant."

The remarkable ability to target one or even a couple of sites on a large protein with a small molecule, under photochemical control, is a considerable challenge and this challenge has been addressed in some depth in this book. Systematic modification of the structure of the photoreagent provided valuable information on the binding site recognition as well as the mechanism of the photocleavage reaction. Some factors that impact the photocleavage reaction include the exact location of the probe binding site on the protein, conformations of the bound probe at the binding site, protein size, functional groups present on the probe that interact with the protein surroundings either in a favorable or unfavorable manner, overall charge on the photoreagent, and photophysical as well as photochemical properties of the probe. The protein photocleavage studies, in all case, were preceded by detailed binding studies by a variety of spectroscopic methods. Methods as simple as absorption and fluorescence spectroscopies or more sophisticated circular dichroism spectroscopy were used. Conclusions that are most consistent with the binding data indicated a single binding site on most proteins, irrespective of the probe or the protein, with only one exception noted so far. Photoactivation of the bound probe resulted in protein cleavage at a single site, in many instances. The specificity for the reaction has been investigated in detail and molecular modeling studies provided a firm ground to rationalize the observed cleavage sites. The reagents provide unique tools for sequencing large proteins by converting them into smaller fragments by non-biochemical transformations. Understanding of the rules for the above methodology are also investigated which provided rational methods for the design of small molecules that could bind at particular sites on large proteins, and this is a major breakthrough for a variety of fields including drug design, protein targeting, mass spectrometry, proteomics and other cutting-edge research areas.

Basics of proteins and proteomics techniques In-depth understanding of mass-spectrometry and quantitative proteomics An overview of interactomics and its application for translational research. Advancement in the field of proteomics and challenges in clinical applications.

Introductory Review on Sirtuins in Biology and Disease provides key insights for scientists and advanced students who need to understand sirtuins and the current research in this field. This book is ideal for pharmaceutical companies as they develop novel targets using sirtuins for metabolic diseases, cancer and neurodegenerative illnesses. Sirtuins are a diverse family of proteins, with several members in mammals. The functional diversity of sirtuins is rather broad, and they have been implicated in various central biological processes. Thus, they are also highly relevant in the context of various human diseases, from cancer to neurodegeneration.

Written primarily for students embarking on an undergraduate bioscience degree, this primer introduces students to the essential topics in protein science clearly and concisely by describing the basic chemical structure of proteins, the factors that stabilize protein structures, protein function, and protein evolution. It begins by placing proteins in their general context in life. They are synthesized as amino-acid sequences encoded in genomes, and fold spontaneously to three-dimensional structures. This is the point where life makes the tremendous leap from the one-dimensional world of genome and amino-acid sequences, to the three-dimensional world of protein structures - indeed, the world which we inhabit. Protein Science prepares readers for later more advanced study of the subject, but will also leave readers who do not go on to such advanced study with a satisfying grasp of the essentials of the subject. Protein Science is supported by online resources and is available for students and institutions to purchase in a variety of formats. The e-book offers a mobile experience and convenient access along with functionality tools, navigation features and links that offer extra learning support: www.oxfordtextbooks.co.uk/ebooks The online resources include: For students: - Self-test questions - Animations of protein structures introduced in the text For registered adopters of the book: * Figures from the book, available to download

This second edition of Protein Purification provides a guide to the major chromatographic techniques, including non-affinity absorption techniques, affinity procedures, non-absorption techniques and methods for monitoring protein purity. The new edition of the book has been organized to encourage incremental learning about the topic, starting with the properties of water, progressing through the characteristics of amino acids and proteins which relate to the purification process. There is an overview of protein strategy and equipment, followed by discussions and examples of each technique and their applications. The basic theory and simple explanations given in Protein Purification make it an ideal handbook for final year undergraduates, and postgraduates, who are conducting research projects. It will also be a useful guide to more experienced researchers who need a good overview of the techniques and products used in protein purification. Key Features * Guide to the major techniques used in protein purification * Includes flowcharts to help the reader slect the best purification strategy * Contains step-by-step protocols that guide the reader through each technique and its use * Includes exercises and solutions

This volume provides an overview of the main yeast production platforms currently used and future yeast cell factories for recombinant protein production. Chapters detail approaches of genetic and metabolic engineering, co-factor containing proteins and virus-like particles, glycoproteins, and post-translational modifications of proteins. 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. Authoritative and cutting-edge, Recombinant Protein Production in Yeast: Methods and Protocols aims to provide state of the art background and methods for protein producing yeast platforms, as well as case studies for special applications.

This book contains an extensive collection of critical reviews, from leading researchers in the field of regulated protein degradation. It covers the role of regulated proteolysis in a range of microorganisms (from Gram positive, Gram negative and pathogenic bacteria to Archaea and the Baker s yeast Saccharomyces cerevisiae)."

Prion Protein, Volume 150, the latest volume in the Progress in Molecular Biology and Translational Science series, focuses on Prion Protein, a protein that is considered to be the archetype of intrinsically disordered proteins. This updated volume includes comprehensive sections on a variety of timely topics, including Functions of Prion Protein, Copper and Prion protein, Cell Biology of Prion Protein, Structural Studies of Prion Proteins, Molecular Simulations on Wild Type and Mutant Prion Proteins, Genetics of Prion Protein, The Prion Concept and Synthetic Prions, and Transgenic Mouse Models. As neurodegenerative diseases represent a health issue that is receiving increasing attention from the scientific community due to their social and economic impact, this series is an ideal resource for the latest research in molecular biology and translational science.

The activity of many biopharmaceutical polymers is dependent on conformation, and the next several years will see increased interest in the conformational analysis of these polymers resulting from the development of biosimilar or "follow-on" biological products. While a wide variety of approaches to analysis exists, finding the most viable ones would be much easier with a consolidated reference that details the benefits and cost of each approach, with an emphasis on real results and real products. Explores the Growing Role of Conformational Analysis in Comparing Generic Biopharmaceuticals Approaches to the Conformational Analysis of Biopharmaceuticals gathers the most useful techniques and methods into a single volume, putting the greatest emphasis on those approaches that have proven the most fruitful. Rather than cover specific uses of techniques in detail, this book provides commercial biotechnologists and researchers with the information and references they need to make good choices about the technology they choose to use. With a large number of references that direct readers to primary source material, it includes studies drawn from the gamut of current literature, covering physical methods, such as differential scanning calorimetry, light scanning, and analytical ultracentrifugation. It also addresses chemical methods, such as hydrogen-deuterium exchange and trace labeling, along with infrared, ultraviolet, and Raman spectroscopy. Written by Roger Lundblad, a true pioneer in protein science, this volume supplies the necessary information researchers need to access when deciding on the most cost-effective approach, including: Comparability of biopharmaceuticals Characterization of follow-on biologics Quality attributes of protein biopharmaceuticals Confrontational analysis of biopharmaceutical products With a clear focus on relevant commercial biotechnology, this book belongs on the shelves of those serious researchers who are paving the way for the next generation of biopharmaceutical polymers.

Cellular adhesion is a fundamental process that influences numerous biological activities such as morphogenesis, cell motility and division, as well as signalling. In addition, adhesion is a process important not only in normal physiology and development, but also in disease states such as tumourigenesis, cardiovascular disease, inflammation and infection. There are a plethora of proteins involved in adhesion-related events with a huge diversity in function. As a result, a wide variety of techniques exist to study adhesion related proteins and processes. In Adhesion Protein Protocols, Third Edition, chapters cover techniques to gain insight into the complex and incompletely understood processes that are involved in cellular adhesion. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Adhesion Protein Protocols, Third Edition will be useful for both those new to the field of adhesion protein research as well as the more experienced scientist.

In her thesis, Sara Bobone outlines spectroscopic studies of antimicrobial peptides (AMPs) which are promising lead compounds for drugs used to fight multidrug resistant bacteria. Bobone shows that AMPs interact with liposomes and she clarifies the structure of pores formed by one of these molecules. These results help us to understand how AMPs are selective for bacterial membranes and how their activity can be finely tuned by modifying their sequence. Findings which solve several conundrums debated in the literature for years. In addition, Bobone uses liposomes as nanotemplates for the photopolymerization of hydrogels - exploiting the self- assembly properties of phospholipids. Bobone was able to trap an enzyme using nanometeric particles, while still allowing its activity by the diffusion of substrates and products through the network of the polymer. The innovative nano devices described in this thesis could solve many of the hurdles still hampering the therapeutic application of protein-based drugs.

With potentially high specificity and low toxicity, biologicals offer promising alternatives to small-molecule drugs. Peptide therapeutics have again become the focus of innovative drug development efforts backed up by a resurgence of venture funds and small biotechnology companies. What does it take to develop a peptide-based medicine? What are the key challenges and how are they overcome? What are emerging therapeutics for peptide modalities? This book answers these questions with a holistic story from molecules to medicine, combining the themes of design, synthesis and clinical applications of peptide-based therapeutics and biomarkers. Chapters are written and edited by leaders in the field from industry and academia and they cover the pharmacokinetics of peptide therapeutics, attributes necessary for commercially successful metabolic peptides, medicinal chemistry strategies for the design of peptidase-resistant peptide analogues, disease classes for which peptide therapeutic are most relevant, and regulatory issues and guidelines. The critical themes covered provide essential background information on what it takes to develop peptide-based medicine from a chemistry perspective and views on the future of peptide drugs. This book will be a valuable resource not only as a reference book for the researcher engaged in academic and pharmaceutical setting, from basic research to manufacturing and from organic chemistry to biotechnology, but also a valuable resource to graduate students to understand discovery and development process for peptide-based medicine.

Physics and the life sciences have established new connections within the past few decades, resulting in biological physics as an established subfield with strong groups working in many physics departments. These interactions between physics and biology form a two-way street with physics providing new tools and concepts for understanding life, while biological systems can yield new insights into the physics of complex systems. To address the challenges of this interdisciplinary area, The Physics of Proteins: An Introduction to Biological Physics and Molecular Biophysics is divided into three interconnected sections. In Parts I and II, early chapters introduce the terminology and describe the main biological systems that physicists will encounter. Similarities between biomolecules, glasses, and solids are stressed with an emphasis on the fundamental concepts of living systems. The central section (Parts III and IV) delves into the dynamics of complex systems. A main theme is the realization that biological systems, in particular proteins, do not exist in unique conformations but can assume a very large number of slightly different structures. This complexity is captured in the concept of a free energy landscape and leads to the conclusion that fluctuations are crucial for the functioning of biological systems. The final chapter of this section challenges the reader to apply these concepts to a problem that appears in the current literature. An extensive series of appendices (Part V) provide descriptions of the key physical tools and analytical methods that have proven powerful in the study of the physics of proteins. The appendices are designed to be consulted throughout the section on protein dynamics without breaking the deductive flow of the logic in the central section of the book.

Immunosensing for Detection of Protein Biomarkers not only introduces the principles, methods, and classification of immunoassay, but also presents the latest achievements in areas such as electrochemical immunosensors, nanoprobe-based immunoassay, chemiluminescence immunoassay, electrochemiluminescent immunoassay, multianalyte immunoassay, optical imaging for immunoassay, signal amplification for immunoassay, and so on. In recent years, immunosensing and immunoassay methods have attracted considerable interest due to their applications in different fields, particularly clinical diagnosis. Although a large number of academic papers in immunosensing and immunoassay have been published in different journals recently, it is still a difficult and time-consuming task for researchers, especially those new to the area, to understand the principles, methods, and research progress of immunosensing. Based on the research experience of the authors and their research groups, this book offers readers with new research ideas to develop immunosensing methodology. As a monograph, it offers deeper and more complete coverage than review papers, which only report certain aspects of progress. Grounded in the research experience of Professor Ju's research group, the book focuses on immunosensing for detection of protein biomarkers, summarizing understanding, research, and practice on immunosensing methodology in detection of protein biomarkers.

This detailed collection covers how the biological functions of histone deacetylases (HDACs) and histone acetyltransferases (HATs) can be detected in various experimental settings, both in vivo and in vitro. The book also covers the generation and specificity of deacetylase inhibitors and how such agents can be used to test experimental hypotheses. Written for the popular Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, HDAC/HAT Function Assessment and Inhibitor Development: Methods and Protocols serves as an ideal guide to this vital area of study.

This book provides a comprehensive coverage of the basic principles of structural biology, as well as an up-to-date summary of some main directions of research in the field. The relationship between structure and function is described in detail for soluble proteins, membrane proteins, membranes, and nucleic acids.There are several books covering protein structure and function, but none that give a complete picture, including nucleic acids, lipids, membranes and carbohydrates, all being of central importance in structural biology.The book covers state-of-the-art research in various areas. It is unique for its breadth of coverage by experts in the fields. The book is richly illustrated with more than 400 color figures to highlight the wide range of structures.

Exploring current themes in modern computational and membrane protein biophysics, this book presents a comprehensive account of the fundamental principles underlying different methods and techniques used to describe the intriguing mechanisms by which membrane proteins function. The book discusses the experimental approaches employed to study these proteins, with chapters reviewing recent crucial structural advances that have allowed computational biophysicists to discern how these molecular machines work. The book then explores what computational methods are available to researchers and what these have taught us about three key families of membrane proteins: ion channels, transporters and receptors. The book is ideal for researchers in computational chemistry and computational biophysics.

This unique volume reviews the beautiful architectures and varying mechanical actions of the set of specialized cellular proteins called molecular chaperones, which provide essential kinetic assistance to processes of protein folding and unfolding in the cell. Ranging from multisubunit ring-shaped chaperonin and Hsp100 machines that use their central cavities to bind and compartmentalize action on proteins, to machines that use other topologies of recognition - binding cellular proteins in an archway or at the surface of a 'clamp' or at the surface of a globular assembly - the structures show us the ways and means the cell has devised to assist its major effectors, proteins, to reach and maintain their unique active forms, as well as, when required, to disrupt protein structure in order to remodel or degrade. Each type of chaperone is beautifully illustrated by X-ray and EM structure determinations at near- atomic level resolution and described by a leader in the study of the respective family. The beauty of what Mother Nature has devised to accomplish essential assisting actions for proteins in vivo is fully appreciable.

The Protein Reviews series serves as a publication vehicle for reviews that focus on crucial contemporary and vital aspects of protein structure, function, evolution and genetics. Volumes are published online first, prior to publication in a printed book. Chapters are selected according to their importance to the understanding of biological systems, relevance to the unravelling of issues associated with health and disease, or impact on scientific or technological advances and developments. Volume 21 presents eight review chapters authored by experts in the related fields. The first chapter covers the enzyme squalene monooxygenase and lipid levels and its relevance in health and disease. Chapter two presents a systematic analysis of the structural and functional aspects of heteromeric solute carriers. The third chapter provides a review of the role of CI- in type IV collagen assembly, function, and disease, including future directions for studies. This is followed by a summary in chapter four about the recent progress on defining the roles of the Slit-Robo signaling in bone metabolism and the possible roles of the interaction between Robo and neural epidermal growth factor-like proteins. Chapter five discusses recent data about the evolutionary aspects on structural differences between humans and the nematode in relation to previous knowledge of core proteins and GAG-attachment sites in Chn and CS proteoglycans of C.elegans and humans. The sixth chapter summarizes the immunochemical character of the IGHV1-69-derived RFs and the recognition mechanism of the IGHV1-69-derived RFs. Chapter seven covers regulated alternative translocation and its role as an emerging mechanism to regulate transmembrane proteins. Finally, chapter eight reviews current progress on IL-36 protein and biology and novel investigative tools. This volume is intended for research scientists, clinicians, physicians and graduate students in the fields of biochemistry, cell biology, molecular biology, immunology and genetics.

The aim of the Protein Reviews is to serve as a publication vehicle for review articles that focus on crucial current vigorous aspects of protein structure, function, evolution and genetics. The volumes will appear online before they are published in a printed book. Articles are selected according to their importance to the understanding of biological systems, their relevance to the unravelling of issues associated with health and disease or their impact on scientific or technological advances and developments. The chapters in volume 18 are authored by experts in the field. They deal with aspects of structure and/or biological activity of selected proteins. The chapters review current research of the following topics: the Mechanism of channel gating and regulation of the activity of calcium-activated chloride channel ANO1, Structure and function of the two-component cytotoxins of Staphylococcus aureus, Membrane Fusion and Infection involving the influenza virus hemagglutinin, The impact of arrhythmogenic mutations through the structural determination of the L-type voltage-gated calcium channel, Discussion of some open questions pertaining to histone post-translational modifications and nucleosome organization in transcriptional regulation, Regulation of the extracellular SERPINA5 (protein C inhibitor) penetration through cellular membranes, Coding of Class I and II aminoacyl-tRNA synthetases, Nephrin phosphorylation in diabetes and chronic kidney injury, The structure-forming juncture in oxidative protein folding and the events in the ER, The polyspecificity of anti-lipid antibodies and its relevance to the development of autoimmunity. This volume is intended for research scientists, clinicians, physicians and graduate students in the fields of biochemistry, cell biology, molecular biology, immunology and genetics.

This book focuses on the development of stapled peptides, a novel molecular modality used to regulate aberrant intracellular protein-protein interactions (PPIs). The author designs and presents a novel helical peptide stabilization methodology by constructing a chiral cross-linker moiety, namely "chiral center induced peptide helicity (CIH)". The book demonstrates that a precisely positioned carbon chiral center on tether can decisively determine the secondary structure of a peptide, and that the R-configured peptide is helical, while the S-configured peptide is non-helical. Further, it reports that helicity-enhanced R isomer peptides displayed significantly enhanced cell permeability and target binding affinity, as well as tumor inhibition efficiency, in comparison to S isomer peptides. The book will not only advance readers' understanding of the basic principle of stapled peptides, but also accelerate the clinical transformation of stapled peptide drugs.

This comprehensive, edited book explores carotenoids and their important functional roles in yeast, bacteria and plants and a profound exposition on the structures of carotenoid molecules, focusing in the first of three parts on the biosynthesis of carotenoids. The regulation of carotenoid biosynthesis in photosynthesis as well as in plant, fruits, storage roots and algae is central to the second part, and discoveries about the function of carotenoids in human health feature in the third and final part. Many helpful illustrations, explanations, overviews and examples help to bring readers up to date on relevant themes including carotenogenic genes, carotenoids in fruits and metabolic engineering. The book explores where carotenoids are synthesized in nature, including in carrots and algae. Contributing expert authors examine enzyme functions and plant models, and analyze the structure of carotenoid molecules. The function of carotenoids in photosynthesis and in photosynthetic organs as well as during fruit ripening are then explored. A whole chapter is dedicated to the latest research on apocarotenoids and further chapters cover interesting and novel themes on plastid development and the epigenetic regulation that affects carotenoid synthesis in plants. The metabolic engineering of carotenoids that has been done in fruits, plants, and seeds is another area that readers can explore, along with evidences on the function of carotenoids in human nutrition, as antioxidants, as in the control of lipid metabolism and in the absorption of carotenoids. This is a highly informative and wide-ranging work which will update researchers in the field, as well as supporting students of plant physiology and biotechnology, as supplementary reading.