This is the second edition of a very well received book that details how the sumoylation system functions and how it modulates numerous cellular activities. SUMO is a post-translational modifier in the ubiquitin super-family that has gained recognition over the last twenty years as an essential and prevalent regulatory molecule. Individual chapters explore the biochemistry, molecular biology, and cell biology of the sumoylation system and its substrate proteins. The book is divided into three themed parts: Molecular Functions (I), Cell Growth Regulation (II), and Diseases (III). Parts I and II focus on the contribution of sumoylation to cellular activities in both the nuclear and cytoplasmic compartments. The nuclear activities covered include nucleic acid metabolism (both RNA and DNA), chromosome structure and replication, and nucleocytoplasmic transport. Cytoplasmic processes presented include regulation of membrane ion channels, general metabolism, and apoptotic signalling. Topics in Part III include the role of sumoylation in developmental abnormalities (craniofacial and cardiovascular), diabetes, neurodegenerative diseases, cancer, and infections with viruses and bacteria. Each of the corresponding chapter authors is an active researcher who has made significant contributions to understanding sumoylation. This second edition provides updates and revisions to most of the original chapters plus adds six new chapters to address important developing areas of sumoylation research. This volume is intended for a scientific audience from undergraduates to independent researchers. The content will serve as both a solid introduction for the novice reader and an in depth treatment for the advanced scholar.

This volume presents relevant background information to understanding the molecular basis governing unconventional protein secretion (UPS), and in particular explores the latest techniques and protocols that have been successfully applied for the study of this topic. Detailed chapters include an overview of conventional and unconventional secretory pathways along with multidisciplinary approaches and methods used for UPS analysis in different organisms. 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, Unconventional Protein Secretion: Methods and Protocols will be useful for all interested in the secretory pathway field as well as applications in cell biology, cell development, biomedical research, and healthcare.

This volume covers an array of techniques available for studying SH2 domains and phosphotyrosine signaling. The book is divided into six parts: Part I outlines the history of SH2, technology development, and cell signaling; Part II focuses on computational approaches and tools used for identification, classification, and predictions of SH2 domain binding partners; Part III details various ways to prepare the SH2 domains as experimental reagents; Part IV presents methods for structural analysis and conventional binding assays using SH2 domains; Part V describes high-throughput and proteomics approaches to aid in analyzing SH2-mediated interactions; and Part VI covers applications for SH2 domain to functional and imaging analyzes. 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, SH2 Domains: Methods and Protocols is a valuable resource for computational biologists, biochemists, structural biologists, cell biologists, pathologists, and people interested in SH2 domains and phosphotyrosine signaling. Researchers who are investigating how protein interaction domain mediate specificity in signaling systems may also find this book informative.

This volume highlights the role of proteostasis in human health and associated disease model systems, reflecting its rising importance which has led to the development of new technologies to obtain insight into underling protein mechanistic events. 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, Proteostasis: Methods and Protocols aims to become a reference book on proteostasis in human health.

This book reviews current techniques used in membrane protein structural biology, with a strong focus on practical issues. The study of membrane protein structures not only provides a basic understanding of life at the molecular level but also helps in the rational and targeted design of new drugs with reduced side effects. Today, about 60% of the commercially available drugs target membrane proteins and it is estimated that nearly 30% of proteins encoded in the human genome are membrane proteins. In recent years much effort has been put towards innovative developments to overcome the numerous obstacles associated with the structure determination of membrane proteins. This book reviews a variety of recent techniques that are essential to any modern researcher in the field of membrane protein structural biology. The topics that are discussed are not commonly found in textbooks. The scope of this book includes: Expression screening using fluorescent proteins The use of detergents in membrane protein research The use of NMR Synchrotron developments in membrane protein structural biology Visualisation and X-ray data collection of microcrystals X-ray diffraction data analysis from multiple crystals Serial millisecond crystallography Serial femtosecond crystallography Membrane protein structures in drug discovery The information provided in this book should be of interest to anyone working in the area of structural biology. Students will find carefully prepared overviews of basic ideas and advanced protein scientists will find the level of detail required to apply the material directly to their day to day work. Chapters 4, 5, 6, 8 and 9 of this book are published open access under a CC BY 4.0 license at link.springer.com.

The role of vitamin A in living organisms has been known throughout human history. In the last 100 years, the biochemical nature of vitamin A and its active derivative, retinoic acid, its physiological impact on growth processes, and the essential details of its mechanism of action have been revealed by investigations carried out by researchers using vertebrate and more recently invertebrate models to study a multiplicity of processes and conditions, encompassing embryogenesis, postnatal development to old age. A wealth of intercellular interactions, intracellular signaling systems, and molecular mechanisms have been described and the overall conclusion is that retinoic acid is essential for life. This book series, with chapters authored by experts in every aspect of this complex field, unifies the knowledge base and mechanisms currently known in detailed, engaging, well-illustrated, focused chapters that synthesize information for each specific area. In view of the recent information explosion in this field, it is timely to publish a contemporary, comprehensive, book series recapitulating the most exciting developments in the field and covering fundamental research in molecular mechanisms of vitamin A action, its role in physiology, development, and continued well-being, and the potential of vitamin A derivatives and synthetic mimetics to serve as therapeutic treatments for cancers and other debilitating human diseases. Volume II is divided into nine chapters contributed by prominent experts in their respective fields. Each chapter starts with the history of the area of research. Then, the key findings that contributed to development of the field are described, followed by a detailed look at key findings and progress that are being made in current, ongoing research. Each chapter is concluded with a discussion of the relevance of the research and a perspective on missing pieces and lingering gaps that the author recommends will be important in defining future directions in vitamin A research.

This Brief is devoted to the CFTR protein and cystic fibrosis, and it provides an updated perspective of the genetic, functional and cellular processes involved in this conformational disorder. Starting with a historical perspective on cystic fibrosis and its clinical features, the author departs into an in-depth description of the biology of the CFTR protein, ending with a discussion on the latest approaches aimed at developing corrective therapies for cystic fibrosis. First the basic aspects of cystic fibrosis as a disorder are addressed, focusing on genetics and mutation prevalence. Then the CFTR protein is discussed in detail: its structure and classification within the ABC transporter superfamily, its biogenesis with membrane insertion and chaperone assisted folding, its glycosylation and how it regulates the endoplasmatic reticulum quality control mechanisms that assess CFTR folding status. Extra attention is given to post-ER trafficking and regulation of membrane stability and anchoring, and to CFTR functions. This is linked to the molecular mechanisms through which different CFTR mutations cause cystic fibrosis. Finally, the different efforts aiming at rescuing the basic defect, most of which aim at repairing CFTR dysfunction, are covered. Through this integrated perspective, readers will obtain a unique insight into this fascinating membrane-bound protein and its associated disease. This Brief appeals to an audience interested in human genetics, protein folding, protein trafficking and physiology.

This Brief explores the chemistry and production technology of a cheese precursor: the cow's milk curd. It explains how different coagulation and treatment methods can be used to obtain various types of cheeses. Parameters such as the type of used milk, the coagulation method, pH value, color, and microbial fermentation have a profound impact on the resulting curd properties, and hence on the cheese. The authors discuss some of the most important parameters, and how their modification can lead to a variety of cheese and dairy products. This Brief also addresses the question, if cheese makers can standardize their production procedures, and what role chemistry may play in that. Another important point addressed here are the sources of failures in the curd production, e.g. in packaging systems. Readers will find selected examples of helpful analytical techniques for studying and evaluating curd quality, and for monitoring the chemical evolution of selected chemical substances or protein aggregation.

In this Brief, Joe Jeffers uncovers the life and works of two-time Nobel Laureate Frederick Sanger. Following Sanger's early life to retirement, Jeffers describes how this celebrated British biochemist became the first person to determine the amino acid sequence of a protein for which he was awarded the Nobel Prize in 1958. Highlighting Sanger's remarkable career, Jeffers describes Sanger's later change in research direction to investigate deoxyribonucleic acids (DNA), work for which Sanger also received the Nobel Prize jointly with Paul Berg and Walter Gilbert in 1980. Joe Jeffers conducted twelve interviews with Sanger over the period of 1999-2009 and he has also spoken to more than 40 of Sanger's colleagues and family members. This brief provides a rigorous yet concise view of Sanger on a personal and scientific level and is suitable for biochemists, historians or the interested layperson.

Due to the paucity of reviews on this subject, this volume aims to be timely and promote additional basic and translational research on these proteins in reproductive system development and function within the fields of Anatomy, Embryology and Cell Biology. The breadth of the work being conducted within Reproduction is exemplified by the contributors to this series who will provide reviews on: Grp78 roles in female reproduction, small heat shock proteins/co-chaperones as players in uterine smooth muscle function, the role of heat shock proteins in sperm function and maternal contribution to oogenesis and early embryogenesis, heat shock factors and testes development, HSP90 in ovarian biology and pathology, and the role of HSP70 in regulation of autophagy in pregnancy and parturition.

The study of proteomics provides researchers with a better understanding of disease and physiological processes in animals. Methods in Animal Proteomics will provide animal scientists and veterinarians currently researching these topics in domestic animals a firm foundation in the basics of proteomics methodology, while also reviewing important advances that will be of interest to established researchers in the field. Chapters will provide practical information on a range of topics including protein identification and separation, bioinformatics, and applications to disease and reproduction research. This text will be written by leading international proteomics experts and essential for researchers in the fields of animal biology and veterinary medicine.

This brief provides a broad overview of protein-engineering research, offering a glimpse of the most common experimental methods. It also presents various computational programs with applications that are widely used in directed evolution, computational and de novo protein design. Further, it sheds light on the advantages and pitfalls of existing methodologies and future perspectives of protein engineering techniques.

Immunoassays Edited by R. Edwards Immunoassays are among the most widely used of analytical techniques and have been applied successfully to an extensive range of substances, from single molecules to whole cells. This book provides key data on all types of immunoassay, including RIA, ELISA and dry surface immunoassays, and on the use of photoluminescent and chemiluminescent labels in immunoassays. Essential information is also given on assay design and data processing. The Essential Data series provides rapid access to the core data required by researchers on a daily basis, in convenient pocket-sized volumes.

A common approach to understanding the functional repertoire of a genome is through functional genomics. With systems biology burgeoning, bioinformatics has grown to a larger extent for plant genomes where several applications in the form of protein-protein interactions (PPI) are used to predict the function of proteins. With plant genes evolutionarily conserved, the science of bioinformatics in agriculture has caught interest with myriad of applications taken from bench side to in silico studies. A multitude of technologies in the form of gene analysis, biochemical pathways and molecular techniques have been exploited to an extent that they consume less time and have been cost-effective to use. As genomes are being sequenced, there is an increased amount of expression data being generated from time to time matching the need to link the expression profiles and phenotypic variation to the underlying genomic variation. This would allow us to identify candidate genes and understand the molecular basis/phenotypic variation of traits. While many bioinformatics methods like expression and whole genome sequence data of organisms in biological databases have been used in plants, we felt a common reference showcasing the reviews for such analysis is wanting. We envisage that this dearth would be facilitated in the form of this Springer book on Agricultural Bioinformatics. We thank all the authors and the publishers Springer, Germany for providing us an opportunity to review the bioinformatics works that the authors have carried in the recent past and hope the readers would find this book attention grabbing.  

Maize is a globally important crop mainly utilized as feed, food and raw material for diverse industrial applications. Among cereals, it occupies third place after rice and wheat and is a staple food for a large segment of population worldwide particularly in the Asian as well as African countries. This monogram discusses various aspects of nutritional quality of maize such as quality protein maize which has been considered as most significant discovery in enhancing nutritional quality of cereals in terms of increasing the concentration of essential amino acids. The biochemistry of starch which is an important industrial product of maize has been discussed in detail. Further, the role of maize oil which is highly regarded for human consumption as it reduces the blood cholesterol concentration has also been elaborated. Naturally, maize is a rich source of carotenoids such as beta-carotene, zeaxanthin, lutein, cryptoxanthin which have highly diverse health benefits ranging from maintaining normal vision to lowering of oxidative stress. The need for biofortification of maize for provitamin A carotenoids and their role in alleviating vision impairments have also been discussed. The effect of various biotic and abiotic stresses particularly carbon dioxide and temperature on quality has been discussed thoroughly. Many value-added products as well as fermented foods that have been produced from maize which is consumed in different forms worldwide are also discussed. The aspects related to the maize application as fodder and as a source of malting have also been covered concisely. Overall, the book provides complete information about various quality aspects of maize. The various stakeholders such as maize researchers, extension specialists, students, teachers as well as farmers will be immensely benefitted from this monogram.

Molecular chaperones are a fundamental group of proteins that have been identified only relatively recently. They are key components of a protein quality machinery in the cell which insures that the folding process of any newly-synthesized polypeptide chain results in the formation of a properly folded protein and that the folded protein is maintained in an active conformation throughout its functional lifetime. Molecular chaperones have been shown to play essential roles in cell viability under both normal and stress conditions. Chaperones can also assist in the unfolding and degradation of misfolded proteins and in disaggregating preformed protein aggregates. Chaperones are also involved in other cellular functions including protein translocation across membranes, vesicle fusion events, and protein secretion. In recent years, tremendous advances have been made in our understanding of the biology, biochemistry, and biophysics of function of molecular chaperones. In addition, recent technical developments in the fields of proteomics and genomics allowed us to obtain a global view of chaperone interaction networks. Finally, there is now a growing interest in the role of molecular chaperones in diseases. This book will provide a comprehensive analysis of the structure and function of the diverse systems of molecular chaperones and their role in cell stress responses and in diseases from a global network perspective.

Tea is an important non-alcoholic beverage plant of the world. Cultivation of tea is very important as it earns revenue for the tea growing nations especially the developing countries such as India. Although conventional breeding is well-established and has contributed significantly for varietal improvement of this plant and other Camellia species with ornamental value, yet applications of biotechnology are required to intervene some of the issues where conventional breeding is restricted particularly for woody plants such as tea. It is note-worthy to mention that some amounts of biotechnology works in several facets of tea and its wild species have also been done. In the present book, a state-of-the-art on various aspects of breeding and biotechnology has been complied in eight chapters. They are: i) Origin and descriptions of health benefits as well as morphological classification as first chapter, ii) Breeding and cytogenetics that comprise with various conventional approaches of varietal improvement of tea along with their genetic resources, iii) Micropropagation which deals with in-depth study of clonal propagation, iv) Somatic embryogenesis along with alternative techniques such as suspension culture, cry-preservation etc. v) Molecular breeding that deals with application of various DNA-based markers, linkage map etc., vi) Genetic transformation and associated factors, vii) Stress physiology complied with various works done in tea along with its wild relatives on abiotic as well as biotic stress, and viii) Functional genomics that describe the various works of molecular cloning and characterizations, differential gene expression, high-throughput sequencing, bioinformatics etc. Importantly, the author has made exclusive tables in most of the chapters that include the summary of the works in particular topic. In a nutshell, the book compiles the work already been done, identifies the problems, analyzes the gaps on breeding and biotechnological works of tea as well as its wild species and discusses the future scope as conclusion. Every effort has been made to include all the published works till June 2013. The book will be a useful resource for post-graduate, doctoral as well post-doctoral students working on tea as well as other woody plants. This will also be useful for the scientists working in the areas of life sciences, genomics, biotechnology and molecular biology.

Pulse Dipolar Electron Spin Resonance: Distance Measurements by Peter P. Borbat, Jack H. Freed.Interpretation of Dipolar EPR Data in Terms of Protein Structure, by Gunnar Jeschke.Site-Directed Nitroxide Spin Labeling of Biopolymers, by Sandip A. Shelke and Snorri Th. Sigurdsson. Metal-Based Spin Labeling for Distance Determination, by Daniella Goldfarb. Structural Information from Spin-Labelled Membrane-Bound Proteins, by Johann P. KLare, Heinz-Jürgen Steinhoff. Structural Information from Oligonucleotides, by Richard Ward and Olav Schiemann. Orientation selective DEER using rigid spin labels, cofactors, metals, and clusters, by Claudia E. Tait, Alice M. Bowen, Christiane R. Timmel, Jeffrey Harmer

Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.

This unique text introduces students and researchers to the world of misfolded proteins, toxic oligomers, and amyloid assemblages, and the diseases of the brain that result. During the past few years the connections between failures in protein quality control and neurological disorders have been reinforced and strengthened by discoveries on multiple fronts. These findings provide novel insights on how amyloidogenic oligomers and fibrils form, interconvert from one state to another, and propagate from cell to cell and region to region. Starting with protein folding and protein quality control basics, the reader will learn how misfolded proteins can cause diseases ranging from prion diseases to Alzheimer's disease and Parkinson's disease to Huntington's disease, amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Authoritative but written in a clear and engaging style, Fundamentals of Neurodegeneration and Protein Misfolding Disorders addresses one of today's forefront areas of science and medicine. The text emphasizes the new groundbreaking biophysical and biochemical methods that enable molecular-level explorations and the conceptual breakthroughs that result. It contains separate chapters on each of the major disease classes. Special emphasis is placed on those factors and themes that are common to the diseases, especially failures in synaptic transmission, mitochondrial control, and axonal transport; breakdowns in RNA processing; the potential role of environmental factors; and the confounding effects of neuroinflammation. The book is ideal for use in teaching at the advanced undergraduate and graduate levels, and serves as a comprehensive reference for a broad audience of students and researchers in neuroscience, molecular biology, biological physics and biomedical engineering.

The book provides an comprehensive overview on biology, genetics and cellular functions of serpins (serine protease inhibitors) in health and disease. With over 1000 members serpins are the most diverse family of protease inhibitors. Latest groundbreaking research findings are presented and broaden the understanding on inhibitory and non-inhibitory serpins, not only in mammalian organisms but also in insects, worms, plants and viruses.

This book covers the state-of-the-art of modern MALDI (matrix-assisted laser desorption/ionization) and its applications. New applications and improvements in the MALDI field such as biotyping, clinical diagnosis, forensic imaging, and ESI-like ion production are covered in detail. Additional topics include MS imaging, biotyping/speciation and large-scale, high-speed MS sample profiling, new methods based on MALDI or MALDI-like sample preparations, and the advantages of ESI to MALDI MS analysis. This is an ideal book for graduate students and researchers in the field of bioanalytical sciences. This book also: * Showcases new techniques and applications in MALDI MS * Demonstrates how MALDI is preferable to ESI (electrospray ionization) * Illustrates the pros and cons associated with biomarker discovery studies in clinical proteomics and the various application areas, such as cancer proteomics

This multi-author contributed volume includes methodological advances and original applications to actual chemical or biochemical phenomena which were not possible before the increased sophistication of modern computers. The chapters contain detailed reviews of the developments of various computational techniques, used to study complex molecular systems such as molecular liquids and solutions (particularly aqueous solutions), liquid-gas, solid-gas interphase and biomacromolecular systems. Quantum modeling of complex molecular systems is a useful resource for graduate students and fledgling researchers and is also an excellent companion for research professionals engaged in computational chemistry, material science, nanotechnology, physics, drug design, and molecular biochemistry.

This book is dedicated to the channels and pores that belong to an eclectic and ubiquitous class of unconventional - perhaps at times strange - pore-forming molecules, which nevertheless play fundamental roles in various organisms. These non-canonical channels may take on various and sometimes complex architectures, such as large beta-barrels or lipid-containing pores. They may originate from bacteria, viruses or intracellular organelles. For some of them, the physiologically relevant substrate may indeed be ions, and for others folded polypeptides. Some are released by cells in a soluble form that has the ability to insert into biological membranes to exert its permeabilizing effect. Many of these unconventional pores have been investigated by electrophysiology, which, by its virtue of focusing on a few or even a single unit, has provided invaluable insight into the mechanisms and structure-function relationships of these remarkable membrane entities. The chapters of this book highlight a representative set of these interesting investigations.

This book covers the latest developments in the physical biology of proteins and peptides. Key insights into microscopic and macroscopic approaches to describe biologically relevant macromolecules and their interactions are provided. This book also covers a wide range of tools, including theoretical methods as statistical mechanics, normal mode analysis, kinetic theory and stochastic processes, and all-atom and coarse-grained molecular dynamics simulations. New experimental techniques are also discussed, particularly related to amiloidogenic peptides and their mutations. This is an excellent book for molecular biologists, physicists, computational scientists, and chemists. It covers cutting-edge research in this exciting, interdisciplinary research field. This book also: Discusses the latest developments in the physical biology of proteins, peptides and enzymes covering theoretical, computational, and experimental approaches Broadens readers' understanding on the r ole of intra- and inter-molecular interactions as a fundamental cornerstone of macroscopic biological properties of macromolecules Provides a wide and useful perspective on different aspects of the physics, biology, and chemistry of proteins and peptides suitable for interdisciplinary research.