This detailed new edition presents the latest developments of the main pillars of protein analysis, namely sample preparation, separation, and characterization. Core areas in this volume are protocols for the analysis of post-translational modifications and protein interaction partners, followed by sophisticated procedures to enrich for extracellular vesicles and organelles, along with several types of protein immuno-assays complemented by various methods for the characterization of antibodies and host-cell protein analysis. Last but not least, a few standard sample preparation protocols and recent advances concerning immuno-chemical detection of proteins are included as well. Written for the highly successful 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, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Proteomic Profiling: Methods and Protocols, Second Edition serves as an ideal reference for students of biochemistry, biomedicine, biology, and genomics and will be an invaluable source for the experienced, practicing scientist as well.

Written by a pioneer in the development of spin labeling in biophysics, this expert book covers the fundamentals of nitroxide spin labeling through cutting-edge applications in chemistry, physics, materials science, molecular biology, and biomedicine. Nitroxides have earned their place as one of the most popular organic paramagnets due to their suitability as inhibitors of oxidative processes, as a means to polarize magnetic nuclei, and, in molecular biology, as probes and labels to understand molecular structures and dynamics AS DRAGS FOR CANCER AND OTHER DISEASES. Beginning with an overview of the basic methodology and nitroxides' 145-year history, this book equips students with necessary background and techniques to undertake original research and industry work in this growing field.

Beginning from centuries of anecdotal descriptions of cell death, such as those on the development of the midwife toad in 1842 by Carl Vogt, to modern-day investigations of cell death as a biological discipline, it has become accepted that cell death in multicellular organisms is a normal part of life.This book provides a comprehensive view of cell death, from its mechanisms of initiation and execution, to its implication in human disease and therapy.

Physiological cell death plays critical roles in almost all aspects of biology, and the book details its roles in lymphocyte homeostasis, neuronal function, metabolism, and the DNA damage response.When physiological cell death goes awry, diseases can arise, and cancer is presented as a central paradigm for the consequences of derangements in the interplay between cell survival and cell death.At the same time, the potential promise of targeted therapies aimed at interdicting cell death machineries are also discussed extensively.The molecular mechanisms that underlie apoptotic cell death are illustrated from the perspectives of both the intrinsic, mitochondrial apoptotic pathway and the extrinsic, death receptor pathway.Key players in these pathways, such as the Bcl2 family proteins, cytochrome c, Apaf-1, caspases, death receptor adapter proteins, and inhibitor of apoptosis proteins, are presented from both functional and structural angles. Until only a few years ago, programmed cell death has been considered essentially synonymous with apoptosis.However, we now know that programmed cell death can also take other forms such as necrosis or necroptosis, and to this end, the mechanisms that underlie programmed necrosis in development and host defense are illustrated.The past twenty plus years have seen an incredible growth of research in cell death, with one breakthrough after another, and the legacy still goes on with constant new surprises and findings.Long live cell death "

This book summarizes all the important aspects of CRLs (Cullin-RING E3 Ubiquitin Ligases), while providing details of mechanistic specifics that go beyond protein ubiquitination and neddylation. Ubiquitin ligases, including the CRLs, which are activated by neddylation, play an important role in diverse biological processes and are involved in various human diseases, particularly cancer. The book covers various topics, such as CRL structure, biology, genetics, its regulation by neddylation, its pivotal role in human disease, and its potential in drug discovery and targeted therapies. The book appeals to biochemists and biologists working in other fields, and, given the importance of CRLs in all aspects of cell biology and the great promise of targeting these complexes for therapy, is a valuable resource anyone interested in modern biology or medicine.

This book, a consecutive contribution to the series Challenges and Advances in Computational Chemistry and Physics, focuses on understanding the photoinduced processes in biological systems. Understanding and fine control of light fate in molecules is vital for the progress of society and environmental safety. Light induced changes of various physico-chemical and spectroscopic properties in nucleic acids and proteins is the basis of fundamental biological events such as vision, DNA photodamage or photosensing. The investigation of these processes is challenging to both theoretical and experimental studies. This volume encompasses the quantum mechanics/molecular mechanics theory in several subfields, including: advanced computational methods for nucleic acids and proteins systems; dynamics, spectroscopic and physico-chemical properties of biological photoreceptors; DNA photodamage. This book is of interest to readers in both fundamental and application-oriented research by overviewing recent achievements in computational modeling of excited states in nucleic acids and proteins.

The complexity and heterogeneity of biological systems has posed an immense challenge in recent years. An increasingly important tool for obtaining molecular and atomic scale information on a range of large biological molecules and cellular components is solid-state NMR. This technique can address fascinating problems in structural biology, including the arrangement of supramolecular complexes and fibril formation in relation to molecular folding, misfolding and aggregation. Advances in Biological Solid-State NMR brings the reader up to date with chapters from international leaders of this growing field, covering the most recent developments in the methodology and applications of solid-state NMR to studies of membrane interactions and molecular motions. A much needed discussion of membrane systems is detailed alongside important developments in in situ analysis. Topics include applications to biological membranes, membrane active peptides, membrane proteins, protein assemblies and in-cell NMR. This exposition of an invaluable technique will interest those working in a range of related spectroscopic and biological fields. A basic introduction invites those interested to familiarise themselves with the basic mathematical and conceptual foundations of solid-state NMR. A thorough and comprehensive discussion of this promising technique follows, which is essential reading for those working or studying at postgraduate level in this exciting field.

This volume contains a collection of innovative techniques for studying targeted protein degradation. Chapters guide readers through heterobifunctional proteolysis-targeting chimeras (PROTACs) approaches, E3 ligase, E3 ligase-induced ubiquitylation, proteomic approaches, novel degrader molecules, molecular glue, and stabilize binding interaction between a target and E3 ubiquitin ligase. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Targeted Protein Degradation: Methods and Protocols aims to ensure successful results in this emerging field of drug discovery.

Widely recognized as one of the most important signaling mechanisms in development and disease, Wnt signaling pathways are networks of proteins that play significant roles in embryogenesis or cancer development. Wnt Signaling in Development and Disease addresses the fundamentals of Wnt signaling and delves into molecular pathway mechanisms, its role in embryogenesis, adult tissue homeostasis, and chronic disease. This comprehensive resource details current knowledge of Wnt signaling while looking ahead to future progress.

This book presents a comprehensive overview of important immune molecules and their structure-function relationships. The immune system is highly complex, consisting of a network of molecules, cells, tissues and organs, and the immune reaction is involved in various physiological as well as pathological processes, including development, self-tolerance, infection, immunity, and cancer. Numerous molecules participate in immune recognition, inhibition and activation, and these important immune molecules can be roughly divided into cell surface receptors, intracellular receptors and intracellular signaling molecules. The study of how these immune molecules function at molecular level has laid the foundation for understanding the immune system. The book provides researchers and students with the latest research advances concerning the structural biology of key immune molecules/pathways, and offers immunologists essential insights into how these immune molecules function.

This volume provides readers with a comprehensive look at the latest techniques used to identify and characterize PDZ-mediated interactions. Chapters cover topics such as promiscuity, multimodularity, regulation, and viral recognition by PDZ domains. 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. Cutting-edge and thorough, PDZ Mediated Interactions: Methods and Protocols is a valuable resource for all researchers interested in learning more about this developing field.

This book provides a single-source reference on the current state of the ribosome profiling method by describing experimental protocols for the quantitative analysis of translation in a variety of model organisms. In addition, the volume presents a detailed overview of the existing software tools and includes detailed description of methods for statistical analysis, data processing, and visualization of ribosome profiling data. Written for the highly successful 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, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Ribosome Profiling: Methods and Protocols aims to provide the type of standardized protocols that have previously been unavailable in an effort to bypass the major barriers to wide use of ribosome profiling-based approaches.

This book offers an authoritative review of biopharmaceuticals and their clinical relevance. Biopharmaceuticals have been showing high therapeutic potential by means of biological and biosimilar medicines, particularly for the treatment of cancer, chronic diseases (e.g. diabetes, Crohn's disease, psoriasis and rheumatoid arthritis), neurodegenerative disorders (e.g. multiple sclerosis), and they have also been contributing to the progress of innovative therapies such as assisted reproductive medicine. Since the eighties, several biopharmaceuticals have been approved and, due to patents expiration, many biosimilars are also marketed. In this book, readers will find the most relevant updated information about the main clinical applications of pharmaceutical biotechnology. The authors provide expert analysis about the industrial challenges of recombinant proteins and the different classes of biopharmaceuticals, including monoclonal antibodies, vaccines, growth factors and stem cells. Topics such as bioprinting technologies in tissue engineering, gene therapy and personalized medicine are also covered in this book. Professionals, students and researchers interested in this field will find this work an important account.

Proteins Biochemistry and Biotechnology 2e is a definitive source of information for all those interested in protein science, and particularly the commercial production and isolation of specific proteins, and their subsequent utilization for applied purposes in industry and medicine. Fully updated throughout with new or fundamentally revised sections on proteomics as, bioinformatics, protein glycosylation and engineering, well as sections detailing advances in upstream processing and newer protein applications such as enzyme-based biofuel production this new edition has an increased focus on biochemistry to ensure the balance between biochemisty and biotechnology, enhanced with numerous case studies. This second edition is an invaluable text for undergraduates of biochemistry and biotechnology but will also be relevant to students of microbiology, molecular biology, bioinformatics and any branch of the biomedical sciences who require a broad overview of the various medical, diagnostic and industrial uses of proteins. Provides a comprehensive overview of all aspects of protein biochemisty and protein biotechnology Includes numerous case studies Increased focus on protein biochemistry to ensure balance between biochemisty and biotechnology Includes new section focusing on proteomics as well as sections detailing protein function and enzyme-based biofuel production "With the potential of a standard reference source on the topic, any molecular biotechnologist will profit greatly from having this excellent book. " ( Engineering in Life Sciences, 2004; Vol 5; No. 5) Few texts would be considered competitors, and none compare favorably." ( Biochemistry and Molecular Education, July/August 2002) "...The book is well written, making it informative and easy to read..." ( The Biochemist, June 2002)

This detailed book gathers a broad collection of experimental approaches to assist researchers in setting up different methods to investigate protein conformational disorders. Beginning with a section on assays focusing on biophysical approaches to study protein (mis)folding, the volume continues with sections on cellular and proteostasis assays as well as assays for protein folding correction and recovery, combining methods such as thermal shift assays, in silico improvement of protein solubility, and compound screening, an important area of research as it may open avenues for therapeutic strategies. Written for the highly successful 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, and tips for troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Misfolding Diseases: Methods and Protocols serves as an ideal guide for researchers seeking to advance our knowledge of protein conformational disorders.

This book is a passionate account of the scientific breakthroughs that led to the solution of the first protein structures and to the understanding of their function at atomic resolution. The book is divided into self-standing chapters that each deal with a protein or protein family. The subject is presented in a fluid, non-technical style that will engage student and scientists in biochemistry, biophysics, molecular and structure biology and physiology.

This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.

Cancer is one of the leading death cause of human population increasingly seen in recent times. Plants have been used for medicinal purposes since immemorial times. Though, several synthetic medicines are useful in treating cancer, they are inefficient and unsafe. However, plants have proved to be useful in cancer cure. Moreover, natural compounds from plants and their derivatives are safe and effective in treatment and management of several cancer types. The anticancer plants such as Catharanthus roseus, Podophyllum peltatum, Taxus brevifolia, Camptotheca acuminate, Andrographis paniculata, Crateva nurvala, Croton tonkinensis, Oplopanax horridus etc., are important source of chemotherapeutic compounds. These plants have proven their significance in the treatment of cancer and various other infectious diseases. Nowadays, several well-known anticancer compounds such as taxol, podophyllotoxins, camptothecin, vinblastine, vincristine, homoharringtonine etc. have been isolated and purified from these medicinal plants. Many of them are used effectively to combat cancer and other related diseases. The herbal medicine and their products are the most suitable and safe to be used as an alternative medicine. Based on their traditional uses and experimental evidences, the anticancer products or compounds are isolated or extracted from the medicinally important plants. Many of these anticancer plants have become endangered due to ruthless harvesting in nature. Hence, there is a need to conserve these species and to propagate them in large scale using plant tissue culture. Alternatively, plant cell tissue and organ culture biotechnology can be adopted to produce these anticancer compounds without cultivation. The proper knowledge and exploration of these isolated molecules or products could provide an alternative source to reduce cancer risk, anti-tumorigenic properties, and suppression of carcinogen activities. Anticancer plants: Volume 1, Properties and Application is a very timely effort in this direction. Discussing the various types of anticancer plants as a source of curative agent, their pharmacological and neutraceutical properties, cryo-preservations and recent trends to understand the basic cause and consequences involved in the diseases diagnosis. We acknowledge the publisher, Springer for their continuous inspiration and valuable suggestions to improvise the content of this book. We further extend our heartfelt gratitude to all our book contributors for their support, and assistance to complete this assignment. I am sure that these books will benefit the scientific communities including academics, pharmaceuticals, nutraceuticals and medical practitioners.

This volume presents an overview of contemporary quantitative proteomics methods along with instructions on data interpretation, while providing examples on how to implement proteomics into systems biology. 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. Thorough and practical, Proteomics in Systems Biology: Methods and Protocols is a valuable resource for researchers who are interested in using proteomics techniques to help answer biological and medical questions.

This second edition integrates the more technical and mathematical aspects of bioinformatics with concrete examples of their application to current research problems in molecular, cellular and evolutionary biology. This broad, unified approach is made possible, in large part, by the very wide scope of Dr. Xia's own research experience. The integration of genomics, proteomics and transcriptomics into a single volume makes this book required reading for anyone entering the new and emerging fields of Systems Biology and Evolutionary Bioinformatics.

After decades of dominance of genetics and genomics, the importance of structural biology is growing exponentially in the field of plant biology. The main objectives of this new book series is to "demystify" structural biology for plant researchers and to provide important insights into the basic molecular mechanisms underlying plant development through the diverse approaches utilized by structural biologists. The book series starts with a theme dedicated to hormonal signaling that has benefited from the application of structural biology. "Plant Structural Biology: Hormonal Regulations" provides up-to-date knowledge of the structural aspects of hormonal signal recognition, signal transduction, hormonal control of downstream regulatory pathways and hormonal crosstalk. The most distinctive features of this book as well as future titles is/will be to provide overview of cutting-edge research in the field of plant structural biology, and to serve as a compendium of various approaches that could be applied to problems being solved in modern plant biology. Last but not least, we hope this book will facilitate and broaden the community of (not only) plant scientists who are interested in structural biology approaches and tools. For these reasons, the style of this series is concise and general, in order to avoiding unnecessary details. Explanatory boxes describing the basics of specific approaches (e.g. X-ray crystallography, NMR, SAXS, molecular dynamics simulations, etc.) are included.

In this book, the author describes the development of the experimental diffraction setup and structural analysis of non-crystalline particles from material science and biology. Recent advances in X-ray free electron laser (XFEL)-coherent X-ray diffraction imaging (CXDI) experiments allow for the structural analysis of non-crystalline particles to a resolution of 7 nm, and to a resolution of 20 nm for biological materials. Now XFEL-CXDI marks the dawn of a new era in structural analys of non-crystalline particles with dimensions larger than 100 nm, which was quite impossible in the 20th century. To conduct CXDI experiments in both synchrotron and XFEL facilities, the author has developed apparatuses, named KOTOBUKI-1 and TAKASAGO-6 for cryogenic diffraction experiments on frozen-hydrated non-crystalline particles at around 66 K. At the synchrotron facility, cryogenic diffraction experiments dramatically reduce radiation damage of specimen particles and allow tomography CXDI experiments. In addition, in XFEL experiments, non-crystalline particles scattered on thin support membranes and flash-cooled can be used to efficiently increase the rate of XFEL pulses. The rate, which depends on the number density of scattered particles and the size of X-ray beams, is currently 20-90%, probably the world record in XFEL-CXDI experiments. The experiment setups and results are introduced in this book. The author has also developed software suitable for efficiently processing of diffraction patterns and retrieving electron density maps of specimen particles based on the diffraction theory used in CXDI.

The Subcellular Biochemistry series has recently embarked upon an almost encyclopaedic coverage of topics relating to the structure and function of macromolecular complexes (Volumes 82, 83 and 87). The present multi-author text covers numerous aspects of current research into molecular virology, with emphasis upon viral protein and nucleoprotein structure and function. Structural data from cryo-electron microscopy and X-ray crystallography is displayed throughout the book. The 17 chapters in the book cover diverse interesting topics, all currently under investigation, contributed by authors who are active actively involved in present-day research. Whilst structural aspects predominate, there is much consideration of the structure-function relationship. In addition, the book correlates with and extends from Volume 68 of the series "Structure and Physics of Viruses: An Integrated Textbook". This book is directed primarily at professionals that work in the broad field of Structural Biology and will be of particular interest to Structural Virologists. The editors, David Bhella and Robin Harris, have much experience in virology and protein structure, respectively. Dr Bhella is Director of the Scottish Macromolecular Imaging Centre. Professor Robin Harris is the long-standing Series Editor of the Subcellular Biochemistry series. He has edited and contributed to several books in the series.

This new edited volume in the Springer Subcellular Biochemistry Series presents a comprehensive, state-of-the-art overview of the proteomics of peroxisomes derived from mammalian, Drosophila, fungal, and plant origin, and contains contributions from leading experts in the field. The development of sensitive proteomics and mass spectrometry technologies, combined with bioinformatics approaches now allow the identification of low-abundance and transient peroxisomal proteins and permits to identify the complete proteome of peroxisomes, with the consequent increase of our knowledge of the metabolic and regulatory networks of these important cellular organelles. The book lines-up with these developments and is organized in four sections including: (i) mass spectrometry-based organelle proteomics; (ii) prediction of peroxisomal proteomes; (iii) analysis of peroxisome proteome interaction networks; and (iv) peroxisomes in relation to other subcellular compartments. The editor Luis A. del Rio is Professor ad honorem of the Spanish National Research Council (CSIC) in the Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry and Cell & Molecular Biology of Plants, at the Estacion Experimental del Zaidin, Granada, Spain. Del Rio's research group focuses on the metabolism of reactive oxygen species (ROS), reactive nitrogen species (RNS) and antioxidants in plant peroxisomes, and the ROS- and RNS-dependent role of peroxisomes in plant cell signalling. The editor Michael Schrader is Professor of Cell Biology & Cytopathology in the Department of Biosciences at the University of Exeter, UK. Using mammalian peroxisomes as model organelles, Prof. Schrader and his team aim to unravel the molecular machinery and signalling pathways that mediate and regulate the formation, dynamics and abundance of these medically relevant cellular compartments.

This book comprehensively reviews the state-of-the-art strategies developed for protein-protein interaction (PPI) inhibitors, and highlights the success stories in new drug discovery and development. Consisting of two parts with twelve chapters, it demonstrates the design strategies and case studies of small molecule PPI inhibitors. The first part discusses various discovery strategies for small molecule PPI inhibitors, such as high throughput screening, hot spot-based design, computational approaches, and fragment-based design. The second part presents recent advances in small molecule inhibitors, focusing on clinical candidates and new PPI targets. This book has broad appeal and is of significant interest to the pharmaceutical science and medicinal chemistry communities.

This book introduces characteristic features of the protein structure prediction (PSP) problem. It focuses on systematic selection and improvement of the most appropriate metaheuristic algorithm to solve the problem based on a fitness landscape analysis, rather than on the nature of the problem, which was the focus of methodologies in the past. Protein structure prediction is concerned with the question of how to determine the three-dimensional structure of a protein from its primary sequence. Recently a number of successful metaheuristic algorithms have been developed to determine the native structure, which plays an important role in medicine, drug design, and disease prediction. This interdisciplinary book consolidates the concepts most relevant to protein structure prediction (PSP) through global non-convex optimization. It is intended for graduate students from fields such as computer science, engineering, bioinformatics and as a reference for researchers and practitioners.