Membrane proteins, representing nearly 40% of all proteins, are key components of cells involved in many cellular processes, yet only a small number of their structures have been determined. Membrane Protein Structure Determination: Methods and Protocols presents many detailed techniques for membrane protein structure determination used today by bringing together contributions from top experts in the field. Divided into five convenient sections, the book covers various strategies to purify membrane proteins, approaches to get three dimensional crystals and solve the structure by x-ray diffraction, possibilities to gain structural information for a membrane protein using electron microscopy observations, recent advances in nuclear magnetic resonance (NMR), and molecular modelling strategies that can be used either to get membrane protein structures or to move from atomic structure to a dynamic understanding of a molecular functioning mechanism. 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 on troubleshooting and avoiding known pitfalls. Comprehensive and easy to use, Membrane Protein Structure Determination: Methods and Protocols serves as an ideal reference for scientists seeking to further our knowledge of these vital and versatile proteins as well as our overall understanding of the complicated world of cell biology.

Protein conversion from a water-soluble native conformation to the insoluble aggregates and fibrils, which can deposit in amyloid plaques, underlies more than 20 human diseases, representing a major public health problem and a scientific challenge. Such a conversion is called protein misfolding. Protein misfolding can also involve errors in the topology of the folded proteins and their assembly in lipid membranes. Lipids are found in nearly all amyloid deposits in vivo, and can critically influence protein misfolding in vitro and in vivo in many different ways. This book focuses on recent advances in our understanding of the role of lipids in modulating the misfolding of various proteins. The main emphasis is on the basic biophysical studies that address molecular basis of protein misfolding and amyloid formation, and the role of lipids in this complex process.

One ofthe major drivers in biological research is the establishment ofstructures and functions of the 50,000 or so proteins in our bodies. Each has a characteristic- dimensional structure, highly "ordered" yet "disordered"! This structure is essential for a protein's function and, significantly, it must be sustained in the competitive and complex environment of the living cell. It is now being recognised that when a cell loses control, proteins can se- assemble into more complex supermolecular structures such as the amyloid fibres and plaques associated with the pathogenesis of prion (CJD) or age-related (Alzheimer's) diseases. This is a pointer to the wider significance of the self-assembling properties of polypeptides. It has been long known that, in silk, polypeptides are assembled into- sheet structures which impart on the material its highly exploitable properties of flexibility combined with high tensile strength. But only now emerging is the recognition that peptides can Self-assemble into a wide variety of non-protein-like structures, including fibrils, fibres, tubules, sheets and monolayers. These are exciting observations and, more so, the potential for materials and medical exploitations is so wide ranging that over 80 scientists from Europe, USA, Japan and Israel. met 1-6 July 1999 in Crete, to discuss the wide-ranging implications of these novel developments. There was a spirit of excitement about the workshop indicative of an important new endeavor. The emerging perception is that of a new class of materials set to become commercially viable early in the 21st century.

Praise for the Series:
"The authority, originality, and editing of the review are first class."
--Nature
"The Advances in Protein Chemistry series has been a major factor in the education of protein chemists."
--Journal of the American Chemical Society

Key Features
* Respiratory metabolism in hyperthermophilic organisms
* Structure and stability of hyperstable proteins
* Thermostable DNA polymerases
* DNA stability and DNA binding proteins
* Hyperthermophiles and their heat-shock proteins

Steroids is a thematic volume from the classic Academic Press series, Vitamins and Hormones. Gerald Litwack, the new editor of this prestigious serial, brings together leading contributors to the study of steroids. These structurally and functionally complex molecules are of interest to a broad cross-section of endocrinologist, cell biologists, and biochemists. Reviews include studies of structure, function, and regulation of steroid production and action. Thus, Vitamins and Hormones continues to publish cutting-edge reviews of interest to endocrinologists and biochemists. Others will increasingly turn to this continuing series for comprehensive reviews by leading researchers in this and related disciplines.

Protein Folding Kinetics - Biophysical Methods (2nd Edition) gives a deep insight into the principles and concepts of the kinetic and structural resolution of fast chemical and biophysical reactions of proteins with emphasis on protein-folding reactions. The study of fast protein-folding reactions and the understanding of the folding paradox have significantly advanced due to the recent development of new biophysical methods which allow not only kinetic resolution in the sub-millisecond time scale but also structural resolution with unprecedented precision. Pathways and structures of early and late folding events and the transition state structures of fast- and ultrafast-folding proteins can now be studied in far more detail. Important techniques include biophysical, chemical, molecular biological and mathematical methods, in particular protein engineering, Phi-value analysis, time-resolved circular dichroism, optical triggers and pulsed infrared LASER methods, pressure and temperature jump, ultrafast mixing, stopped flow and quenched flow, dielectric relaxation and electric-field-jump, acoustic relaxation, fluorescence- and isotope-labeling, H/D exchange methods, NMR line broadening and stopped-flow NMR, transition state theory, solutions of rate equations, and evolutionary computer programming. Protein Folding Kinetics - Biophysical Methods is written for students and researchers in biochemistry, biophysics, and related fields.

Special features in the second edition:

-Includes detailed information and 12 color figures on the high resolution of folding transition states.

-Discusses structural determinants of the rate of protein folding on a timescale from microseconds to seconds.

-Provides information on self-evolving computer programs for protein-folding simulations and protein-structure predictions.

Blurb for Volume 1
Hans Vogel and a panel of leading researchers review the protein chemistry and behavior of this significant protein class, and provide a comprehensive collection of proven experimental techniques for their study both in vitro and in vivo. This first volume discusses the role of calcium in intracellular secondary messenger activation mechanisms, including unique aspects of calcium chemistry and its utilization in diary proteins and blood clotting. Detailed case studies provide a wealth of valuable information about protein purification and characterization strategies, X-ray crystallography, and specific calcium-binding proteins and their modes of action. The second companion volume focuses on cutting-edge experimental methods for studying solution structure, stability, dynamics, calcium-binding properties, and biological activity of calcium-binding proteins in general.
Single Blurb for Both Volumes:
Hans Vogel and a panel of leading researchers review the protein chemistry and behavior of this significant protein class, and provide a comprehensive collection of proven experimental techniques for their study both in vitro and in vivo. The first volume discusses the role of calcium in intracellular secondary messenger activation mechanisms, including unique aspects of calcium chemistry and its utilization in dairy proteins and blood clotting. Detailed case studies provide a wealth of valuable information about protein purification and characterization strategies, X-ray crystallography, and specific calcium-binding proteins and their modes of action. The second volume focuses on cutting-edge experimental techniques for studying the solution structure, stability, dynamics, calcium-binding properties, and biological activity of calcium-binding protein in general. In addition to enzymatic assays and more routine spectroscopic and protein chemistry techniques, there are also NMR approaches, thermodynamic analyses, kinetic measurements such as surface plasmon resonance, strategies for amino acid sequence alignments, and fluorescence methods to study the distribution of calcium and calcium-binding proteins in cells.

Protein kinase CK2 (formerly casein kinase II or 2) is known to play a critical role in the control of cell growth and cell death and is thus intimately involved in the development of cancer. More specifically, CK2 has been found to be elevated in all cancers examined. While CK2 levels are known to be high in proliferating normal cells, CK2 has also been found to be a potent suppressor of apoptosis and is a link to the cancer cell phenotype, which is characterized by deregulation of both cell proliferation and cell death. Indeed, it would appear that CK2 impacts many of the hallmarks of cancer and it has now gained considerable attention as a potential target for cancer therapy. Protein Kinase CK2 and Cellular Function in Normal and Disease States increases knowledge of the role of CK2 in the development of cellular dysfunction and emphasizes that this protein may serve as a target of drug development for improved cancer therapy. In addition, it is a handy tool that provides cancer researchers, graduate students, and all scientists involved in CK2 research with one main source for the latest advances in CK2 research.

This detailed volume explores advances in vector design, DNA delivery, cell cultivation, host cell engineering, and bioprocess optimization within the study of recombinant protein expression in mammalian cells. The majority of the protocols employ either Chinese hamster ovary cells (CHO) or human embryonic kidney 293 cells (HEK293), the workhorses of the field, as the production host; however, the methods can be adapted to other mammalian hosts under the appropriate cell-specific conditions. 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 convenient, Recombinant Protein Expression in Mammalian Cells: Methods and Protocols aims to aid researchers in building on our knowledge of protein structure and function and to speed the discovery of new therapeutic proteins.

The synthesis of proteins from 20 or so constituent amino acids according to a strictly defined code with an accuracy of better than 1 in 10,000 at most loca tions is arguably the most complex task performed by cells. Protein Synthesis collects together methods and protocols covering a range of different approaches towards understanding how the cellular machinery accomplishes this task and how these ftinctions might be harnessed by the biotechnology industry to generate novel and useful proteins. The era in which the components of the translational machinery were being catalogued is over. This volume gathers together protocols that focus on preserving and describing the dynamic function as closely as possible. The need to understand exactly how ribosomes are positioned on messages or where tRNA molecules, translation factors, or control proteins are bound, has been appreciated by many of the authors. Several chapters that explore the fidelity and processivity of translation reflect this belief. Moreover, the fundamental importance of rRNA at the heart of the ribosome is a strong theme in a number of the protocols. These articles include in vitro and in vivo systems from bacterial, fungal, plant, and animal systems. Overall, Protein Synthesis might be characterized by the novelty of the approaches employed to illuminate the inner workings of the protein synthetic machinery as well as by the inventiveness of the attempts to harness these reactions for biotechnological applications."

In an ever-increasing domain of activity Amino Acids Peptides and Proteins provides an annual compilation of the world's research effort into this important area of biological chemistry. Volume 30 provides a review of literature published during 1997. Comprising a comprehensive review of significant developments at this biology/chemistry interface each volume opens with an overview of amino acids and their applications. Work on peptides is reviewed over several chapters ranging from current trends in their synthesis and conformational and structural analysis to peptidomimetics and the discovery of peptide-related molecules in nature. The application of advanced techniques in structural elucidation is incorporated into all chapters whilst periodic chapters on metal complexes of amino acids, peptides and beta-lactams extend the scope of coverage. Efficient searching of specialist topics is facilitated by the sub-division of chapters into discrete subject areas allowing annual trends to be monitored. All researchers in the pharmaceutical and allied industries and at the biology/chemistry interface in academia will find this an indispensable reference source.

After a little more than 20 years since the original discovery of neuropeptide Y (NPY) by Tatemoto and colleagues, the field of NPY research has made remarkable progress and is coming of age.The present volume addresses all major topics in connection with NPY and related peptides by established leaders in their respective areas. Experienced NPY-aficionados will certainly find new and useful additional information in this volume and newcomers to the field will hopefully discover how much exciting research this still has to offer.

Protein engineering is a fascinating mixture of molecular biology, protein structure analysis, computation, and biochemistry, with the goal of developing useful or valuable proteins. Protein Engineering Protocols will consider the two general, but not mutually exclusive, strategies for protein engineering. The first is known as rational design, in which the scientist uses detailed knowledge of the structure and function of the protein to make desired changes. The s- ond strategy is known as directed evolution. In this case, random mutagenesis is applied to a protein, and selection or screening is used to pick out variants that have the desired qualities. By several rounds of mutation and selection, this method mimics natural evolution. An additional technique known as DNA shuffling mixes and matches pieces of successful variants to produce better results. This process mimics recombination that occurs naturally during sexual reproduction. The first section of Protein Engineering Protocols describes rational p- tein design strategies, including computational methods, the use of non-natural amino acids to expand the biological alphabet, as well as impressive examples for the generation of proteins with novel characteristics. Although procedures for the introduction of mutations have become routine, predicting and und- standing the effects of these mutations can be very challenging and requires profound knowledge of the system as well as protein structures in general.

In this book leading researchers in the field discuss the state-of-the-art of many aspects of SAPK signaling in various systems from yeast to mammals. These include various chapters on regulatory mechanisms as well as the contribution of the SAPK signaling pathways to processes such as gene expression, metabolism, cell cycle regulation, immune responses and tumorigenesis. Written by international experts, the book will appeal to cell biologists and biochemists.

Assisting Oxidative Protein Folding: How Do Protein Disulphide-Isomerases Couple Conformational and Chemical Processes in Protein Folding?, by A. Katrine Wallis and Robert B. Freedman Peptide Bond cis/trans Isomerases: A Biocatalysis Perspective of Conformational Dynamics in Proteins, by Cordelia Schiene-Fischer, Tobias Aumuller and Gunter Fischer Small Heat-Shock Proteins: Paramedics of the Cell, by Gillian R. Hilton, Hadi Lioe, Florian Stengel, Andrew J. Baldwin und Justin L. P. Benesch Allostery in the Hsp70 Chaperone Proteins, by Erik R. P. Zuiderweg, Eric B. Bertelsen, Aikaterini Rousaki, Matthias P. Mayer, Jason E. Gestwicki and Atta Ahmad Hsp90: Structure and Function, by Sophie E. Jackson Extracellular Chaperones, by Rebecca A. Dabbs, Amy R. Wyatt, Justin J. Yerbury, Heath Ecroyd and Mark R. Wilson"

TLR4 is one of the most important innate immunity receptors, its function mainly consisting in the activation of inflammatory pathways in response to stimulation by Pathogen-Associated Molecular Patterns (PAMPs) and Damage Associated Molecular Pattern molecules (DAMPs). This volume critically reviews the different types of TLR4 activators and inhibitors, discusses the role of molecular aggregates in agonism/antagonism as well as the pivotal role of the CD14 receptor in the modulation of TLR4 signal and the molecular details and actors of the intracellular cascade. The book presents the role of TLR4 in several pathologies, such as sepsis and septic shock caused by receptor activation by gram-negative bacterial lipopolysaccharide (LPS), in neurodegenerative and neurological diseases such as Parkinson and Alzheimer's diseases, and Amyotrophic Lateral Sclerosis (ALS). It reviews the role of TLR4 in neural stem cell-mediated neurogenesis and neuroinflammation and in Human Induced Pluripotent Stem Cells and Cerebral Organoids and discusses the emerging role of micro-RNA (miRNA) regulation by TLR4.

Molecular chaperones are involved in a wide variety of essential cellular processes in living cells. A subset of molecular chaperones have been initially described as heat shock proteins protecting cells from stress damage by keeping cellular proteins in a folding competent state and preventing them from irreversible aggregation. Later it became obvious that molecular chaperones are also expressed constitutively in the cell and are involved in complex processes such as protein synthesis, intracellular protein transport, post-translational modification and secretion of proteins as well as receptor signalling. Hence, it is not surprising that molecular chaperones are implicated in the pathogenesis of many relevant diseases and could be regarded as potential pharmacological targets. Starting with the analysis of the mode of action of chaperones at the molecular, cellular and organismic level, this book will then describe specific aspects where modulation of chaperone action could be of pharmacological and therapeutic interest.

Protein-protein interactions (PPIs) are strongly predictive of functional relationships among proteins in virtually all processes that take place in the living cell. Therefore, the comprehensive exploration of interactome networks is one of the major goals in systems biology. The aim of Two Hybrid Technologies: Methods and Protocols is to provide a compendium of state-of-the art protocols for the investigation of binary PPIs with the classical yeast two-hybrid (Y2H) approach, Y2H variants and other in vivo methods for PPI mapping. Divided into two convenient sections, the first gives a survey of protocols that are currently employed for Y2H high-throughput screens by different expert labs in the field. Rather than detailing the principles of screening, which have been described previously, the focus is on different implementations of Y2H interactome mapping. The second section of the book considers innovative PPI detection methods that have the potential to emerge as alternative high-throughput methodologies. 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, Two Hybrid Technologies: Methods and Protocols supplies researchers with a comprehensive toolbox for the identification of biologically relevant protein interactions.

With the invitation to edit this volume, I wanted to take the opportunity to assemble reviews on different aspects of circadian clocks and rhythms. Although most c- tributions in this volume focus on mammalian circadian clocks, the historical int- duction and comparative clocks section illustrate the importance of various other organisms in deciphering the mechanisms and principles of circadian biology. Circadian rhythms have been studied for centuries, but only recently, a mole- lar understanding of this process has emerged. This has taken research on circadian clocks from mystic phenomenology to a mechanistic level; chains of molecular events can describe phenomena with remarkable accuracy. Nevertheless, current models of the functioning of circadian clocks are still rudimentary. This is not due to the faultiness of discovered mechanisms, but due to the lack of undiscovered processes involved in contributing to circadian rhythmicity. We know for example, that the general circadian mechanism is not regulated equally in all tissues of m- mals. Hence, a lot still needs to be discovered to get a full understanding of cir- dian rhythms at the systems level. In this respect, technology has advanced at high speed in the last years and provided us with data illustrating the sheer complexity of regulation of physiological processes in organisms. To handle this information, computer aided integration of the results is of utmost importance in order to d- cover novel concepts that ultimately need to be tested experimentally.

The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.

When I received an invitation from Ron Landes (Landes Bioscience) to edit a book on CtBP family proteins, I was gratified to realize that the importance of these proteins has reached the level of deserving a 'separate' book. As the reader can see, there has been significant advancement in our understanding of the fijnctions of these proteins in the past ten years since CtBPl was cloned in our laboratory. Genetic and biochemical studies with Drosophila provided the critical evidence to show that dCtBP is a transcriptional CO repressor. Genetic studies with mutant mice have established that these proteins are essential for animal development. The CtBP family proteins are unique in several aspects. They were the first among proteins containing a metabolic enzyme fold to be implicated in transcriptional regulation. The vertebrate CtBPs exhibit distinct nuclear and cytosolic activities. The crystal struaures of CtBPl and molecular modeling studies have illuminated the mo- lecular basis of its dual activity and the interaction with target peptides. The organization of the vertebrate CtBP2 gene has provided a novel example of genomic consolidation indicating how a single gene could code for two di- verse proteins. I believe that this book will be a valuable reference source for new researchers to understand more about the CtBP family proteins and their role in growth, development and oncogenesis.

In an ever-increasing domain of activity Amino Acids Peptides and Proteins provides an annual compilation of the world's research effort into this important area of biological chemistry. Volume 29 provides a review of literature published during 1996. Comprising a comprehensive review of significant developments at this biology/chemistry interface each volume opens with an overview of amino acids and their applications. Work on peptides is reviewed over several chapters ranging from current trends in their synthesis and conformational and structural analysis to peptidomimetics and the discovery of peptide-related molecules in nature. The application of advanced techniques in structural elucidation is incorporated into all chapters whilst periodic chapters on metal complexes of amino acids, peptides and beta-lactams extend the scope of coverage. Efficient searching of specialist topics is facilitated by the sub-division of chapters into discrete subject areas allowing annual trends to be monitored. All researchers in the pharmaceutical and allied industries and at the biology/chemistry interface in academia will find this an indispensable reference source.

From the Reviews of the Previous Volumes
"The authority, originality, and editing of the reviews are first class."
-NATURE
"The Advances in Protein Chemistry series has been a major factor in the education of protein chemists."
-JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

With the end of the Human Genome Project in sight, the next important step is to determine the function of genes. Proteome Research is an important approach to this study and is the first book to comprehensively cover the application of two-dimensional electrophoresis, the central methodology in proteome research. The state-of-the-art is described in detail and the available detection methods are extensively covered. Sufficient detail is given to allow readers to apply these technologies to their own particular requirements.

In this thesis, the author investigates the chemistry and application of molecules containing urea and amide bonds. These bonds are some of the strongest known and are fundamental to biological processes. The author describes his discovery that sterically hindered ureas undergo solvolysis at room temperature under neutral conditions. This is a remarkable finding, since ureas are inert under these conditions and a general rule of chemistry is that hindered substrates are less reactive. Remarkably, the author translates these results to the correspondingly sterically hindered amides. This thesis has resulted in a number of outstanding publications in high profile journals. The unique method for breaking urea and amide bonds developed in this study is likely to have far reaching consequences for biological protein manipulation.