This volume aims to provide protocols on a wide range of biochemical methods, analytical approaches, and bioinformatics tools developed to analyze the proteome. 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, Proteomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

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 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.

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.

Transcriptomics and proteomics, studying the profile of the expression of nucleic acids and proteins respectively, are increasingly applied to gain a mechanistic insight into a wide spectrum of investigation, and the use of expression profiling studies for the central nervous system and brain function aids in the understanding of neurodegenerative disorders and tumor development mechanisms. In Expression Profiling in Neuroscience, expert researchers provide a survey of the most commonly used approaches in the field and scan the different ways of studying the central nervous system/brain environment through expression profiling. The first part addresses the gene expression profiling of the brain at a large scale or to a specific cell type such as blood-brain barrier endothelium. Then, the second part describes the protein expression studies and the different technologies applied. Written for the popular Neuromethods series, chapters include corresponding background information, tested laboratory protocols, and step-by-step methods for reproducible laboratory experiments. Detailed and authoritative, Expression Profiling in Neuroscience presents the state-of-the-art techniques necessary to expand research further into this vital area of study.

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.

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.

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.

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.

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

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.

Professor Fox's multi-volume Advanced Dairy Chemistry set was first published in four volumes in the early 1980s. A second edition came out in the early 1990s, and an updated third edition was published a decade later. The set is the leading major reference on dairy chemistry, providing in-depth coverage of milk proteins, lipids, and lactose. The editors propose beginning the revision cycle again, with a revised first volume on proteins, to be divided and published separately as Volume 1A - Proteins: Basics Aspects, and Volume 1B - Applied Aspects. Fox and his co-editor, Paul McSweeney, have created an extensively revised the Table of Contents for Volume 1A, which details the novel and updated chapters to be included in this upcoming fourth edition. New contributors include highly regarded dairy scientists and scholars from around the world.

Proteins act as macromolecular machinery that mediate many diverse biological processes - the molecular mechanisms of this machinery has fascinated biologists for decades. Analysis of the kinetic and thermodynamic features of these mechanisms could reveal unprecedented aspects of how the machinery function and will eventually lead to a novel understanding of various biological processes. This dissertation comprehensively demonstrates how two universally conserved guanosine triphosphatases in the signal recognition particle and its membrane receptor maintain the efficiency and fidelity of the co-translational protein targeting process essential to all cells. A series of quantitative experiments reveal that the highly ordered and coordinated conformational states of the machinery are the key to their regulatory function. This dissertation also offers a mechanistic view of another fascinating system in which multistate protein machinery closely control critical biological processes. Written while completing graduate work at California Institute of Technology.

1 a a 4 17 10 15 ubiquitin; and of 16 VCP 17 18 20 33 34 34 36 p domain. 41 42 42 43 P U 42 47 binding. C. elegans 16 In 21 22 50 51 52 53 13 and UFD 4 10 of Cdc48. 18 30 of Ufd2. COFACTORS 47 23 13 47 47 47 72 15 15 and of Spt23 p90. Ufd2 and Cdc48. In C. elegans 74 16 75 75 76 76 Ufd2 25 54 54 7 56 p47 7 7 80 30 30 81 82 82 but and CD3 26 DUB COFACTORS 30 UFD3 OTU1 4 Cdc48 30 4 OLE1. 15 27 87 REFERENCES 30 REGULATION OF UBIQUITIN MONOUBIQUITINATION UBIQUITINATION 1 32 7 S) d 33 12 13 14 15 18 19 15 20 21 35 15 15 27 15 31 32 31 33 36 monoubiquitination of pol pol 34 37 34 monoubiquitination. 20 35 trans 3 15 REFERENCES by monoubiquitination. Mol Cell; 2009. UBIQUITIN LIGASE ACTIVITY BY Nedd 1 2 of 41 5 6 8 fold. 9 13 14 edd 43 18 18 K M and k 18 22 23 K M 24 25 K M 26 edd 45 18 27 K M K D 18 25 . 8 10 M 21 28 MECHANISM AND REGULATION OF CRLs 34 41 34 edd 47 48 S. pombe 49 51 p27 and I by SCF and SCF 57 58 59 60 CTD CTD CTD CTD in Cul5 CTD CTD CTD 60 18

Over the past decade, there has been an explosive development of research of intrinsically disordered proteins (IDPs), which are also known as unfolded proteins. Structural biologists now recognize that the functional diversity provided by disordered regions complements the functional repertoire of ordered protein regions. In Intrinsically Disordered Protein Analysis: Methods and Experimental Tools, expert researchers explore the high abundance of IDPs in various organisms, their unique structural features, numerous functions, and crucial associations with different diseases. Volume 2 includes sections on single molecule techniques, methods to assess protein size and shape, analyzing conformational behavior, mass-spectrometry, expression and purification of IDP's. Written in the highly successful Methods in Molecular Biology (TM) series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Intrinsically Disordered Protein Analysis: Methods and Experimental Tools helps scientists further their investigations of these fascinating and dynamic molecules.

This volume is comprised of a collection of experimental protocols for common techniques and strategies used to study the biogenesis of b-barrel outer membrane proteins in Gram-negative bacteria. The BAM Complex: Methods and Protocols guides readers through methods on the function of the BAM complex, the roles played by each of the individual components, the expression and purification of the components, crystallization and structure determination of the components, and how the individual Bam components may assemble into a functional complex. 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, The BAM Complex: Methods and Protocols will serve as an invaluable reference for those interested in studying the BAM complex.

This volume focuses on screening and profiling kinase inhibitors or activators. Chapters in this book cover several facets of the drug discovery processes starting with target identification, and assay development and screening chemical libraries for hit identification and lead optimization. The profiling portion of Kinase Screening and Profiling: Methods and Protocols discusses several strategies and techniques that are required to minimize off target hits and reduce cellular toxicities that are caused by liability kinases. 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. Timely and authoritative, Kinase Screening and Profiling: Methods and Protocols, will benefit scientists and researchers who are interested in exploring the role of kinases in academic, as well as pharmaceutical research.

This volume highlights recent developments in flow cytometry, affinity assays, imaging, mass spectrometry, microfluidics and other technologies that enable analysis of proteins at the single cell level. The book also includes chapters covering a suite of biochemical and biophysical methods capable of making an entire gamut of proteomic measurements, including analysis of protein abundance or expression, protein interaction networks, post-translational modifications, translocation and enzymatic activity. 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 thorough, Single Cell Protein Analysis: Methods and Protocols is useful to researchers and students in biological and biomedical sciences who have an interest in proteomic measurements in cells.

Exploring the 2-D gel mapping field, the chapters in this book are separated into four different categories: Part I talks about 2-D maps reproducibility and maps modeling; Part II describes the image analysis tools that provide spot volume datasets; Part III is about the statistical methods applied to spot volume datasets to identify candidate biomarkers; and Part IV discusses differential analysis from direct image analysis tools. 2-D PAGE Map Analysis: Methods and Protocols provides a unique approach to 2-D gel mapping, in that it helps users avoid drawbacks due to ignorance of the basic theoretical mechanisms underlying the technique, including data handling and proper tools for spot analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, 2-D PAGE Map Analysis: Methods and Protocols, is a useful resource for any scientist or researcher, with a mathematical background, who is interested in 2-D gel mapping.

This expert volume provides insights into the technological fundamentals together with a comprehensive overview of the potentialities of peptide microarray technology in basic research and clinical assays. Advancements made in recent years in peptide library synthesis, immobilization chemistry and array production have created a foundation from which different new applications are derived, extending the ways in which peptide microarray technology is applied every day. Divided into three sections, the book covers cutting-edge methods and technology, chemoselective strategies for peptide immobilization, and peptide microarrays for medical applications. Written for the high 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 protocols and tips on troubleshooting and avoiding known pitfalls. Fully updated and authoritative, Peptide Microarrays: Methods and Protocols, Second Edition seeks to encourage scientists to apply current peptide array protocols to the study of interesting new biochemical and medical questions and to assist researchers aiming at developing new methods to further develop peptide microarray technology.

This second edition provides up-to-date protocols focusing on techniques for the specific enrichment of phosphopeptides and phosphoproteins. Phosphoproteomics Methods and Protocols, Second Edition guides readers through different labeling strategies for quantitative phosphoproteomics; high-throughput mass spectrometry-based phosphoproteome analyses and phospho flow cytometry; and bioinformatics strategies for phosphoproteomics data analysis and integration. Additional protocols concentrate on the identification of kinase-substrate relationships by both high- and low-throughput approaches. 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, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Phosphoproteomics Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

This detailed volume focuses on methods for the characterization of aggregation processes that lead to the formation of amyloid fibrils and amyloid oligomers which feature in the etiology of a variety of human disorders collectively known as amyloidoses. The scope of the collection includes techniques for visualizing early steps on the amyloid formation pathway, methods for capturing and characterizing oligomeric, potentially toxic, intermediates, strategies for preparing and characterizing mature amyloid fibrils and approaches for understanding templating and transmission of amyloid aggregates. Written in the highly successful Methods in Molecular Biology series format, the 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, Protein Amyloid Aggregation: Methods and Protocols serves as an ideal guide for biochemists and biophysicists with an interest in elucidating the mechanisms of protein amyloid formation, as well as chemists, pharmacologists and clinicians with an interest in leveraging an understanding of such mechanisms for the purpose of therapeutic development.