The second edition of p53 Protocols expands upon the first edition with progress in p53 research since the publication of the first edition. In p53 Protocols, Second Edition expert researchers in the field detail many of the methods that address the challenging questions of the p53 field. These methods include the identification of the target genes and binding partners of gain of function p53 mutants, methods to determine stress response, autophagy or senescence induced by p53, cell cycle analysis, analysis of different phases of DNA replication modified by p53, and generation of pluripotent stem cells. 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, p53 Protocols, Second Edition seeks to aid scientists in the further study into p53 and other tumor suppressors.

Providing current diverse approaches and techniques used to study the immunoproteome, Immunoproteomics: Methods and Protocols collects chapters from key researchers that deliver information to be used in diagnostics, disease progression, and vaccine correlates of protection analysis, to name but a few. This detailed volume includes techniques used for the study of the antibody targets of bacterial pathogens, viruses, and cancer, mass spectrometry-based approaches to characterize T-cell epitopes, chapters on detection and relative quantification of cytokines in serum, as well as in silico prediction of epitopes using sequence-based or modeling 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, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and thorough, Immunoproteomics: Methods and Protocols aids researchers in transferring these techniques to their own laboratories in addition to providing a reference to guide researchers toward appropriate techniques.

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.

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

Protein analysis is increasingly becoming a cornerstone in deciphering the molecular mechanisms of life. Proteomics, the large-scale and high-sensitivity analysis of proteins, is already pivotal to the new life sciences such as Systems Biology and Systems Medicine. Proteomics, however, relies heavily on the past and future advances of protein purification and analysis methods. DIGE, being able to quantify proteins in their intact form, is one of a few methods that can facilitate this type of analysis and still provide the protein isoforms in an MS-compatible state for further identification and characterization with high analytical sensitivity. Differential Gel Electrophoresis: Methods and Protocols introduces the concept of DIGE and its advantages in quantitative protein analysis. It provides detailed protocols and important notes on the practical aspects of DIGE with both generic and specific applications in the various areas of Quantitative Proteomics. Divided into four concise sections, this detailed volume opens with the basics of DIGE, the technique and its practical details with a focus on the planning of a DIGE experiment and its data analysis. The next section introduces various DIGE methods from those employed by scientists world-wide to more novel methods, providing a glance at what is on the horizon in the DIGE world. The volume closes with an overview of the wide range of DIGE applications from Clinical Proteomics to Animal, Plant, and Microbial Proteomics applications. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Differential Gel Electrophoresis: Methods and Protocols can be used by novices with some background in biochemistry or molecular biology as well as by experts in Proteomics who would like to deepen their understanding of DIGE and its employment in many hyphenations and application areas. With its many protocols, applications, and methodological variants, it is also a unique reference for all who seek fundamental details on the working principle of DIGE and ideas for possible future uses of DIGE in novel analytical approaches.

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.

This first of two volumes provides a general overview of the genetics, structure, mechanism and regulation of the Ras superfamily proteins and describes in detail the signaling pathways and processes regulated by specific members of this family. The focus of this first volume is on the Rho and Ras subfamily of small G proteins. Renowned scientists provide insights into the biochemistry of the classical and non-classical small G-protein family members, their spatio-temporal regulation, their effectors and their roles in health and disease. Together with Volume 2, this book provides a comprehensive and state-of-the-art work on small G-proteins (GTPases). It is intended for graduates and professors in biochemistry and cell biology already working on small G-proteins (small GTPases), but also offers an extremely valuable resource for those readers who are new to the field.

Caspases, Paracaspases, and Metacaspacses: Methods and Protocols is a collection of laboratory protocols covering current methods that are employed to measure and detect activities of these proteases in diverse biological systems, ranging from unicellular organisms to mammals. Broken into two parts, the first part focuses on methods to measure, detect, and inhibit activation and activity of a subset of or specific caspases in vitro and in several model systems and organisms, primarily in the context of programmed cell death. The second part of the book provides experimental protocols for purification and in vitro and in vivo analysis of yeast, protozoan and plant metacaspases, as well as of a human paracaspase MALT1. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Authoritative and practical, Caspases, Paracaspases, and Metacaspacses: Methods and Protocols seeks to aid scientists easy-to-follow techniques.

Through all of the recent progress provided by high throughput DNA sequencing technologies, it has become clearer and clearer that the study of proteins and protein organelles will be the key to unlocking our ability to manipulate cells and intervene in human disease. In Protein Expression in Mammalian Cells: Methods and Protocols, expert researchers in the field present a compendium of vital techniques to further our knowledge of mammalian protein expression. 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 tips for troubleshooting and avoiding known pitfalls. Authoritative and concise, Protein Expression in Mammalian Cells: Methods and Protocols will aid scientists seeking to delve deeper into our own biology through the medium of other mammalian cells and proteins.

Amyloid diseases are characterized by the deposition of insoluble fibrous amyloid proteins. The word "amyloid" indicates a starch-like compound, and though a misnomer, continues to be the accepted term for this group of protein conformational disorders. The second edition of Amyloid Proteins expands upon the previous edition with current, detailed protocols for the preparation of amyloid and its precursors, specific analytical methods for studying these proteins, cell culture models and assays for production of amyloid proteins, and protocols for amyloid extraction from tissue, its detection in vitro and in vivo, as well as nontransgenic methods for developing amyloid mouse models. 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, Amyloid Proteins, Second Edition seeks to aid scientists in the amyloid field to establish new techniques in their laboratories. Authoritative and practical, Amyloid Proteins, Second Edition seeks to aid scientists in the amyloid field to establish new techniques in their laboratories.

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.

Despite considerable variability within the scientific community, allosteric regulation can best be defined functionally as how a macromolecule binds one ligand differently when a second ligand is or is not pre-bound to the macromolecule, which constitutes a vital aspect of protein structure/function. In Allostery: Methods and Protocols, expert researchers in the field provide key techniques to investigate this biological phenomenon. Focusing on heterotropic systems with some coverage of homotropic systems, this volume covers the monitoring of allosteric function, allosteric conformational changes, and allosteric changes in protein dynamics/sub-population distribution, as well as topics such as macromolecular and ligand engineering of allosteric functions and computational aids in the study of allostery. 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, Allostery: Methods and Protocols aids scientists in continuing to study ligand-induced, through-protein effects on protein function (ligand binding/catalysis), a phenomenon that is well recognized through the history of the life sciences and very poorly understood at the molecular level.

Super secondary structure(SSS) helps to understand the relationship between primary and tertiary structure of proteins. In Protein Supersecondary Structure: Methods and Protocols expert researchers in the field detail the usefulness of the study of super secondary structure in different areas of protein research. This is done through four main studies SSS representation, SSS prediction, SSS and protein folding, and other application of SSS concept to protein biology. 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 Supersecondary Structure: Methods and Protocols highlight some of the major advances in the many fast-growing areas of supersecondary structure research.

'Antibacterial Surfaces' covers the advances being made in the design of antibacterial surfaces, which have the ability to either prevent the initial attachment of bacterial cells, or kill any cells that come into contact with these surfaces. This book discusses the mechanisms associated with the attachment of bacteria to surfaces and the main strategies currently being employed to control the initial attachment processes. These strategies are expanded upon in the subsequent chapters, where the definition and description of antibacterial surfaces are clarified, as are the mechanisms that come into play when determining the effectiveness of an antibacterial surface. Subsequent chapters discuss a number of naturally occurring antibacterial surfaces, the methods currently being used for producing synthetic antibacterial surfaces, and the current and potential applications of such materials. This book will be of great interest to people who work with materials that need to remain free of bacterial films, from designing safer biomedical implants to the production of self-cleaning materials where the prevention of biofilm formation has significant economic advantages.

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.

The proteome consists of a complex mixture of proteins each of which need to be folded correctly in order to function for the health of the organism, and many of these proteins require molecular chaperones to reach the correct conformation and, in some cases, to remain in a folded form. In Molecular Chaperones: Methods and Protocols, expert researchers address a wide variety of approaches to the study these mechanisms, featuring the workings of heat shock proteins and heat shock transcription factors, in vitro and in vivo. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters features 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, Molecular Chaperones: Methods and Protocols serves as an ideal guide for all scientists who wish to pursue this vital biological action and its impact on human health and disease.

This second of two volumes discusses subfamily proteins which function in molecular and vesicular transport mechanisms inside the cell. In this volume the focus lies on the Rab, Ran and Arf subfamily members. As in Volume 1, the book is written by international renowned scientists in the field of small G-proteins. In elaborate reviews, biochemistry, structure, function and G-protein - effector interactions are described. Together with Volume 1 this book provides an comprehensive state-of-the-art work on small G-proteins (GTPases). It is written for Graduates and Professors in Biochemistry and Cell Biology interested in the mechanism and function of small G-proteins but are extremely valuable for those who want to move into the field.

Diabetes has long been recognized as a disease of high blood sugar, and there has been a continuous search of the exact reason for its development and effective treatment. In 2005, the World Health Organization had estimated that more than 180 million people worldwide suffer from diabetes mellitus and indicated that this figure is likely to double within the next 20 years. Among the 3.8 million deaths each year associated with diabetes, about two thirds are attributable to cardiovascular complications, and diabetes is now considered to be a major metabolic risk factor for the occurrence of heart disease. Diabetic Cardiomyopathy: Biochemical and Molecular Mechanisms is a compilation of review articles devoted to the study on the topic with respect to biochemical and molecular mechanisms of hyperglycaemia. The wide range of areas covered here is of interest to basic research scientists, clinicians and graduate students, who are devoted to study the pathogenesis of diabetes-induced cardiovascular dysfunction. Furthermore, some chapters are directed towards increasing our understanding of novel ways for the prevention/treatment of cardiomyopathy. Twenty five articles in this book are organized in three sections. The first section discusses general aspects of the metabolic derangements in diabetic cardiomyopathy including metabolic alterations and substrate utilization as well as cardiac remodelling in the heart; role of diet in the development of metabolic syndrome in the heart; effect of hyperglycaemia in terms of biochemical and structural alterations in heart. In the second section, several cellular and molecular mechanisms are discussed indicating that diabetic cardiomyopathy is a multifactorial and complex problem. The third section discusses the prevention and treatment of diabetes using appropriate diet, proper supplements including antioxidants, angiotensin inhibitors and some other drugs. All in all, this book discusses the diverse mechanisms of diabetic cardiomyopathy with some information on new therapeutic approaches for finding solutions to prevent or reverse the development of cardiac dysfunction.

ss-barrel outer membrane channel proteins (OMP) are useful as robust and flexible models or components in nanotechnology. Over the last decade biotechnological techniques allowed to expand the natural characteristics of OMPs by modifying their geometry and properties. The present book is oriented towards a broad group of readers including graduate students and advanced researchers. It gives a general introduction to the field of OMP based nano-component development as well as the state of the art of the involved research. On the example of the E. coli FhuA the transformation of an OMP into a tailored nano-channel will be outlined. An exhaustive description of the scientific strategy, including protein selection, analytical methods and "in-silico" tools to support the planning of protein modifications for a targeted application, consideration on the production of a custom made OMP, and an overview on technological applications including membrane/polymersome technology, will be provided.

Protein Structure Prediction, Third Edition expands on previous editions by focusing on software and web servers. With new chapters that provide instructions on how to use a computational method with examples of prediction by the method. 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 protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Protein Structure Prediction, Third Edition provides diverse methods detailing the expansion of the computational protein structure prediction field.

Exploring these type II trans-membrane proteins, The TNF Superfamily: Methods and Protocols focuses on various techniques to investigate aspects of the TNF Superfamily members in health and disease. Opening with protocols to understand the signaling process of TNF family members, this detailed volume continues with technical examples of investigating the role of TNF family members in physiopathologies, protocols on modulation of TNF signaling by pathogens, experimental applications of TNF-reporter mice, as well as methodologies for various assays of TNF family members and the production of recombinant molecules. Written for the 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. Practical and ready to use, The TNF Superfamily: Methods and Protocols will aid researchers investigating this key family of proteins, involved in vital processes such as providing signals for activation, differentiation, survival and death of cells, modulation of immune response and inflammation, hematopoiesis and osteoclastogenesis.

Expert authors provide critical, in-depth reviews of available methods for retrieving selective information out of complex biological systems. Sensors, probes and devices are present and future tools of medicinal diagnostics, environmental monitoring, food analysis and molecular biology. These are based on fluorescence, electrochemistry and mass spectrometry. Coverage of this volume includes sensor development for the detection of small analytes, monitoring of biomolecular interactions, analysis of cellular function, development of diagnostic tools.

Computational modeling can provide a wealth of insight into how energy flow in proteins mediates protein function. Computational methods can also address fundamental questions related to molecular signaling and energy flow in proteins. Proteins: Energy, Heat and Signal Flow presents state-of-the-art computational strategies for studying energy redistribution, signaling, and heat transport in proteins and other molecular machines. The first of four sections of the book address the transport of energy in molecular motors, which function through a combination of chemically driven large-scale conformational changes and charge transport. Focusing on vibrational energy flow in proteins and nanostructures, the next two sections discuss approaches based on molecular dynamics simulations and harmonic analysis. By exploring the flow of free energy in proteins, the last section examines the conformational changes involved in allosteric transitions and the role of coupled protein-solvent dynamics in conformational changes. It also presents computational approaches developed to locate pathways between protein structures. The integrated presentation of this comprehensive, up-to-date volume emphasizes the interrelations between disparate computational approaches that have contributed to our understanding of energy flow in proteins and its role in protein function. By defining the forefront of research in this area, the book delineates the current challenges and opportunities in developing novel methods and applications for the evolving study of energy flow in molecular machines and nanomaterials.

ATP Binding Cassette (ABC) transporters are a family of integral membrane proteins that are likely to be represented in all the cells of all species of archaea, eubacteria and eukaryota. The vast majority of these proteins control the transport of molecules (from small hydrophilic ions to lipids and proteins) across cellular membranes. The human genome encodes 48 ABC transporters and most have been shown to underlie one or more human diseases. This book - that brings together state-of-the-art knowledge on proteins in one volume - will provide students, professors and medical professionals with a background to the human ABC transporters that are known to be relevant to diseases. Each of the 14 chapters is written by a leading researcher in the field and includes contributions from Joe Bryan and Lydia Aguilar-Bryan, Kazu Ueda, Jack Riordan and Robert Tamp . The genetics, structure and function of the proteins, and the future direction of research including the implications for human health are discussed in depth.

This book demonstrates the potential of urine as a biomarker resource for early disease detection, covering the related theory, strategies, tools and findings. Biomarkers are measurable changes associated with diseases. Blood, as a critical part of its internal environment, is closely monitored and controlled by the body to maintain homeostasis, especially in the early stages of diseases. In contrast, urine, as a form of waste excreted by the body, collects a variety of substance changes. Accordingly, urine can offer an ideal resource for early biomarker discovery. In addition, urine is more stable than blood in vitro, and is easy to store and analyze. The book discusses exciting preliminary applications of urine biomarkers for diseases affecting major biological systems. Its main goal is to make scientists, clinicians and medical companies aware of this important, exciting, undeveloped, and profitable field.