Since the publishing of the first edition, the methodologies and instrumentation involved in the field of mass spectrometry-based proteomics has improved considerably. Fully revised and expanded, Mass Spectrometry Data Analysis in Proteomics, Second Edition presents expert chapters on specific MS-based methods or data analysis strategies in proteomics. The volume covers data analysis topics relevant for quantitative proteomics, post translational modification, HX-MS, glycomics, and data exchange standards, among other topics. Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Updated and authoritative, Mass Spectrometry Data Analysis in Proteomics, Second Edition serves as a detailed guide for all researchers seeking to further our knowledge in the field of proteomics.

Molecular farming is a biotechnological approach that includes the genetic adjustment of agricultural products to create proteins and chemicals for profitable and pharmaceutical purposes. Plant molecular farming describes the manufacture of recombinant proteins and other biologically active product in plants. This approach depends on a genetic transformation of plants that can be accomplished by the methods of stable gene transfer, such as gene transfer to nuclei and chloroplasts, and unstable transfer methods like viral vectors. The requirement for recombinant proteins in terms of quality, quantity, and diversity is increasing exponentially This demand is traditionally met by recombinant protein construction technologies and the engineering of orthodox expression systems based on bacteria or mammalian cell cultures. However, majority of developing countries cannot afford the high costs of medicine derived from such existing methods. Hence, we need to produce not only the new drugs but also the cheaper versions of those already present in the market. Plant molecular farming is considered as a cost-effective technology that has grown and advanced tremendously over the past two decades. This book summarizes the advances and challenges of plant molecular farming for all those who are working on or have an interest in this rapidly emerging area of research.

This book highlights current approaches and future trends in the use of mass spectrometry to characterize protein therapies. As one of the most frequently utilized analytical techniques in pharmaceutical research and development, mass spectrometry has been widely used in the characterization of protein therapeutics due to its analytical sensitivity, selectivity, and specificity. This book begins with an overview of mass spectrometry techniques as related to the analysis of protein therapeutics, structural identification strategies, quantitative approaches, followed by studies involving characterization of process related protein drug impurities/degradants, metabolites, higher order structures of protein therapeutics. Both general practitioners in pharmaceutical research and specialists in analytical sciences will benefit from this book that details step-by-step approaches and new strategies to solve challenging problems related to protein therapeutics research and development.

The essential question that fractal dimensions attempt to answer is about the scales in Nature. For a system as non-idealistic and complex as a protein, studying scale-invariance becomes particularly important.

"Fractal Symmetry of Protein Exterior" investigates the diverse facets of the various scales at which we describe protein biophysical and biochemical phenomena. Although these ideas are entirely mathematical, mathematical expositions have been avoided, unless the use of some expressions becomes absolutely obligatory. A first chapter introduce into fractal dimensions, protein exteriors and to methods to study the roughness of surfaces. The main topics covered in the following chapters include: protein-protein interaction interfaces; protein surface-roughness and local shape as well as adhesion on protein and other rough biomolecular surfaces.

With the advent of proteomics came the development of technologies, primarily mass spectrometry, which allowed high-throughput identification of proteins in complex mixtures. While the mass spectrometer resides at the heart of proteomics, its ability to characterize biological samples is only as good as the sample preparation and data analysis tools used in any study. In Proteomics for Biomarker Discovery, expert researchers in the field detail many of the methods which are now commonly used to study proteomics. These include methods and techniques include both label-free approaches and those that utilize stable isotopes incorporated both during cell growth or added via a chemical reaction once the proteome is extracted from the cell. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Proteomics for Biomarker Discovery seeks to aid scientists in the further study the different sample preparation and data analysis tools used in proteomics today.

Chemokines constitute a large family of structurally similar cytokines that contain a signature of conserved cysteine residues joined by disulfide bridges. Binding of chemokines to specific G protein-coupled receptors followed by downstream signaling defines their biological function. Initially, chemoattraction was the key function linked to chemokines/chemokine receptors; however, in recent years, it has become clear that chemokine ligand-receptor interactions can also modulate cellular activation, survival, and proliferation, among other functions in homeostatic and diseased states. Importantly, major advances in our understanding of chemokine biology have led to chemokine receptors becoming specific therapeutic targets with great potential. In Chemokines: Methods and Protocols, expert researchers provide practical information regarding experimental models and state of the art protocols used to delineate chemokine/chemokine receptor function and their applications in health and disease. 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. Practical and easy to use, Chemokines: Methods and Protocols aims to reveal key protocols of functional and descriptive chemokine ligand/receptor assays that will be of practical significance to graduate students, post-doctoral fellows, trainees, and researchers in academia and industry.

This Brief provides a concise review of chaperonopathies, i.e., diseases in which molecular chaperones play an etiologic-pathogenic role. Introductory chapters deal with the chaperoning system and chaperoning teams and networks, HSP-chaperone subpopulations, the locations and functions of chaperones, and chaperone genes in humans. Other chapters present the chaperonopathies in general, including their molecular features and mechanistic classification into by defect, excess, or mistake. Subsequent chapters discuss the chaperonopathies in more detail, focusing on their distinctive characteristics: primary or secondary; quantitative and/or qualitative; structural and hereditary or acquired; genetic polymorphisms; gene dysregulation; age-related; associated with cancer, chronic inflammatory conditions, and autoimmune diseases. The interconnections between the chaperoning and the immune systems in cancer development, chronic inflammation, autoimmunity, and ageing are outlined, which leads to a discussion on the future prospects of chaperonotherapy. The latter may consist of chaperone gene and protein replacement/supplementation in cases of deficiency and of gene or protein blocking when the chaperone actively promotes disease. The last chapter presents the extracellular chaperones and details on how the chaperone Hsp60 is secreted into the extracellular space and, thus, appears in the blood of cancer patients with potential to participate in carcinogenesis and chronic inflammation and autoimmunity. Chaperones as clinically useful biomarkers are mentioned when pertinent. Likewise, guidelines for clinical evaluation of chaperonopathies and for their histopathological and molecular identification are provided throughout. The book also provides extensive bibliography organized by chapter and topic with comments. "

The pleasant community of Limone suI Garda provided outstanding hospitality for a second NATO ARW dealing with apolipoprotein variants, which are natures clues for the discovery of the physiological roles of apolipoproteins in lipoprotein metabolism in normal subjects and patients with specific dyslipoproteinemias. Limone, the site of discovery of the first human apolipoprotein mutant, apoA-I-Milano, provided a brilliant sunny spring venue for more than 50 participants from both sides of the ocean. The attendance at the colorful opening ceremony of the ARW was one of the largest on record. Two members of the Italian government, the Secretaries of Health and the Navy, gave the welcoming addresses. Six television networks, two with national audiences, covered the international workshop. The Limone oracles provided a montage of insights gleamed from the eyes of the clinican, the biochemist, and the molecular biologist. The cumulative information on the molecular defects in lipoprotein metabolism reviewed by this diverse group of investigators provided an ever expanding horizon of new knowledge in this fast moving and some times perplexing field. Clinical vignettes were presented on patients from throughout the world including Canada (Connelly), Turkey (Schmitz), and France (Infante) detailing the clinical sequelae of a defect in a specific apolipoprotein. The clinical importance of Lp(a), a lipoprotein relegated almost to obscurity for many years, has now taken v center stage.

This thesis describes research into the mode of function, inhibition, and evolution of the ribosomal catalytic center, the Peptidyl Transferase Center (PTC)--research that has already led to attempts at improving PTC antibiotics. The PhD candidate carried out two parallel studies. One using a combination of X-ray crystallography, biochemistry, molecular biology, and theoretical studies to obtain crystal structures of ribosomal particles with antibiotics that target the PTC, revealing the modes of action, resistance, cross-resistance and discrimination between ribosomes of eubacterial pathogens and eukaryotic hosts. In the second parallel study, the candidate synthesized a ribosomal substructure--one that may represent the minimal entity capable of catalyzing peptide bond formation--shedding light on the origin of the ribosome itself.

Knowledge of the extracellular matrix (ECM) is essential to understand cellular differentiation, tissue development, and tissue remodeling. This volume of the series "Biology of Extracellular Matrix" provides a timely overview of the structure, regulation, and function of the major macromolecules that make up the extracellular matrix. It covers topics such as collagen types and assembly of collagen-containing suprastructures, basement membrane, fibronectin and other cell-adhesive glycoproteins, proteoglycans, microfibrils, elastin, fibulins and matricellular proteins, such as thrombospondin. It also explores the concept that ECM components together with their cell surface receptors can be viewed as intricate nano-devices that allow cells to physically organize their 3-D-environment. Further, the role of the ECM in human disease and pathogenesis is discussed as well as the use of model organisms in elucidating ECM function.

The use of proteomics to study complex diseases such as cardiovascular disease, the leading cause of death in developed countries, has grown exponentially in recent years. Proteomics is a rapidly expanding investigation platform in cardiovascular medicine and is becoming integrated and incorporated into cardiovascular research. The proteomics field continues to develop with major improvements in mass spectrometry instrumentation, methodology and data analysis. Heart Proteomics: Methods and Protocols complies a selection of techniques and methods that target the numerous processes implicated in the pathophysiology of heart. Chapters cover protocols and updated methods in the heart proteomic area with a particular focus on MS-based methods of protein and peptide quantification and the analysis of posttranslational modifications as well as descriptions of system biology approaches, which provide a better understanding of normal and pathological processes. Written in the successful Methods in Molecular Biology (TM) 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, Heart Proteomics: Methods and Protocols is a representative selection of methods that will prove to be a useful resource for experienced proteomics practitioners and newcomers alike.

This work presents a snapshot of the state of the art of modern biomolecular crystallography, from crystallisation through structure determination and even interactive presentation on the web. Methods driving the latest automated structure determination pipelines are explained, as well as how to deal with problems such as crystal pathologies that still demand expert analysis. These methods are illustrated through their application to problems of great biological interest, such as the molecular machinery underlying the complement pathway, the mechanism of action of monoamine oxidase inhibitors, and the structure of the eukaryotic ribosome. Complementary approaches, such as neutron diffraction, small angle X-ray scattering, coherent diffraction and computational modelling, are also explored.

This work presents a snapshot of the state of the art of modern biomolecular crystallography, from crystallisation through structure determination and even interactive presentation on the web. Methods driving the latest automated structure determination pipelines are explained, as well as how to deal with problems such as crystal pathologies that still demand expert analysis. These methods are illustrated through their application to problems of great biological interest, such as the molecular machinery underlying the complement pathway, the mechanism of action of monoamine oxidase inhibitors, and the structure of the eukaryotic ribosome. Complementary approaches, such as neutron diffraction, small angle X-ray scattering, coherent diffraction and computational modelling, are also explored.

Proteomics is a rapidly expanding investigation platform in cardiovascular medicine. Driven by major improvements in mass spectrometry (MS) instrumentation and data analysis, the proteomics field has flourished in recent years particularly in the study of complex diseases. These recent advances are characterized by the development of quantitative MS-based methods that promoted the field from primarily identifying proteins to also providing measurements of relative changes in protein levels between different cell states. This progress is reflected in the application of proteomic techniques to vascular pathology. Vascular Proteomics: Methods and Protocols provides up-to-date methods and protocols for the analysis of arteries, cells, lipoproteins, body fluids, and metabolites, with a particular focus on MS-based methods of protein and peptide quantification. Written in the successful Methods in Molecular Biology (TM) 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, Vascular Proteomics: Methods and Protocols is a representative selection of methods that can be a useful resource for experienced proteomics practitioners as well as newcomers interested in becoming acquainted with the practice of proteomic techniques for cardiovascular research.

The motivation for us to conceive this series of volumes on regulation was mainly our belief that it would be fun, and at the same time productive, to approach the subject in a way that differs from that of other treatises. We thought it might be interesting and instructive for both author and reader-to examine a particular area of investigation in a framework of many different problems. Cutting across the traditional boundaries that have separated the subjects in past volumes on regulation is not an easy thing to do-not because it is difficult to think of what interesting topics should replace the old ones, but because it is difficult to find authors who are willing to write about areas outside those pursued in their own laboratories. Anyone who takes on the task of reviewing a broad area of interest must weave together its various parts by picking up the threads from many different laboratories, and attempt to produce a fabric with a meaningful design. Finding persons who are likely to succeed in such a task was the most difficult part of our job. In the first volume of this treatise, most of the chapters dealt with the mechanisms of The second volume involved a somewhat regulation of gene expression in microorganisms. broader area, spanning the prokaryotic-eukaryotic border. Topics ranged from phage mor phogenesis to the role of gradients in development. The last volume-Volume 3A-con cerned hormones, as does this volume-Volume 3B.

Kisspeptin has been shown to be both necessary and sufficient for activation of the reproductive axis, during puberty and later in adulthood. This makes kisspeptin a fundamental component of the reproductive axis. Kisspeptin has been deemed the single most potent stimulator of GnRH neurons yet known. The importance of kisspeptin has been documented in humans as well as non-human animal models, ranging from monkeys, sheep, and rodents to numerous fish species, thus signifying a highly conserved nature of its reproductive function. Importantly, kisspeptin neurons seem to mediate many of the regulatory effects of other signals, whether they are metabolic, circadian, hormonal, or stress. This places kisspeptin neurons in a unique position to be key nodal points and conduits for conveying numerous endogenous and exogenous signals to the reproductive axis.

Since the first edition of Protein Nanotechnology Protocols Instruments and Applications the intersection of protein science and nanotechnology has become an exciting frontier in interdisciplinary sciences. The second edition of Protein Nanotechnology Protocols Instruments and Applications expands upon the previous editions with current, detailed chapters that provide examples of proteins which are now being harnessed for a wide range of applications, some more developed than others. This book also delves into engineering proteins and an overview of the sorts of tools that are now readily available to manipulate the structure and function of proteins, both rationally and using methods inspired by evolution. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Nanotechnology Protocols Instruments and Applications, Second Edition seeks to provide an overview of this multi-faceted field and a useful guide to those who wish to contribute to it.

This book contains 14 original review chapters each yielding new, exciting and intriguing data about the emerging understanding of nucleolar structure and function in normal, stressed and diseased cells. The goal of this work is to provide special insight into the nucleolus of the past, present and future, as well its regulation, translocation, and biomedical function. A multitude of topics are introduced and discussed in detail, including nucleologenesis, nucleolar architecture, nucleolar targeting, retention, anchoring, translocation, and the relationship between the nucleolus and cancer. This book also brings together work from several different species, from human to Drosophila to Dictyostelium and other eukaryotic microbes. The final chapter summarizes some of the issues brought up in the various chapters with a view to future research. This book supports the continued emergence of the nucleolus as a dynamic intranuclear region that oversees a vast diversity of events.

This book can be used to provide insight into this important application of biophysics for those who are planning a career in protein therapeutic development, and for those outside this area who are interested in understanding it better. The initial chapters describe the underlying theory, and strengths and weaknesses of the different techniques commonly used during therapeutic development. The majority of the chapters discuss the applications of these techniques, including case studies, across the product lifecycle from early discovery, where the focus is on identifying targets, and screening for potential drug product candidates, through expression and purification, large scale production, formulation development, lot-to-lot comparability studies, and commercial support including investigations.

Biological membranes are the essential structuring elements of all living cells. Many enzymatic reactions take place at the membrane-water interface. To gain detailed insight into membrane properties, it is therefore of great importance to understand the complex nature of the interactions of membrane proteins with lipids. Lipid-Protein Interactions: Methods and Protocols provides a selection of protocols to examine protein-lipid interactions, membrane and membrane protein structure, how membrane proteins affect lipids and how they are in turn affected by the lipid bilayer and lipid properties. The methods described here are all actively used, complementary, and necessary to obtain comprehensive information about membrane structure and function. They include label-free approaches, imaging techniques and spectroscopic methodologies. Written in the successful Methods in Molecular Biology (TM) 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, Lipid-Protein Interactions: Methods and Protocols seeks to serve both professional and novices with its wide range of the methods frequently used in this area of research.

Thousands of proteins have been identified to be acetylated. Immense research power has been dedicated to experiments to solve the biological implications of each and every protein acetylation. Two particular sites of protein acetylation have been described intensively: the N-terminal methionine residue of a nascent protein and lysine residues within a protein. In Protein Acetylation: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study protein acetylation. These include methods and techniques for identification of protein acetylation, column- and gel electrophoresis-based approaches, computationally prediction, and the biological response to protein acetylation. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Acetylation: Methods and Protocols seeks to aid scientists in the further study of the technical aspects involved in understanding protein acetylation.

"Bioinformatics of Human Proteomics" discusses the development of methods, techniques and applications in the field of protein bioinformatics, an important direction in bioinformatics. It collects contributions from expert researchers in order to provide a practical guide to this complex field of study. The book covers the protein interaction network, drug discovery and development, the relationship between translational medicine and bioinformatics, and advances in proteomic methods, while also demonstrating important bioinformatics tools and methods available today for protein analysis, interpretation and predication. It is intended for experts or senior researchers in the fields of clinical research-related biostatistics, bioinformatics, computational biology, medicine, statistics, system biology, molecular diagnostics, biomarkers, or drug discovery and development. Dr.Xiangdong Wang works as a distinguished professor of Respiratory Medicine at Fudan University, Shanghai, China. He serves as Director of Biomedical Research Center, Fudan University Zhongshan Hospital and adjunct professor of Clinical Bioinformatics at Lund University, Sweden. His main research is focused on the role of clinical bioinformatics in the development of disease-specific biomarkers and dynamic network biomarkers, the molecular mechanism of organ dysfunction and potential therapies.

The book is dedicated to the topical area of biology and medicine and the role of stress proteins HSP70 in the regulation of intracellular protein homeostasis, signaling transduction and cell protection. The book is divided into chapters, which describe the discovery of HSP70 and its molecular structure, the mechanism of the synthesis and function in normal and damaged cells, examine the role of HSP70 in immunity, cancerogenesis, aging, Alzheimer's disease and cardiac surgery. In this book, the author looks at HSP70 as a factor which prevents the transformation of homeostasis mechanisms of intracellular proteins into a link in the pathogenesis of a disease.

A major direction in medical research leading to clinical applications targets the regulation of intracellular calcium and the various human diseases associated with an altered homeostasis of this global second messenger. These diseases include, for example: cardiomyopathy, inflammation, brain disorders, diabetes and cancer. In Calcium-Binding Proteins and RAGE: from Structural Basics to Clinical Applications,expert researchers in the field detail many of the methods which are now commonly used to study calcium binding proteins. These methods and techniques, such as calcium-measurements, screening methods, clinical chemistry, and therapy, are generally applicable to many other areas of basic and medical research as well as to diagnostics. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical,Calcium-Binding Proteins and RAGE: from Structural Basics to Clinical Applications underlines the diagnostic and clinical importance of this family of proteins in human diseases and as drug targets.