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."

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 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.

This book summarizes all the important aspects of CRLs (Cullin-RING E3 Ubiquitin Ligases), while providing details of mechanistic specifics that go beyond protein ubiquitination and neddylation. Ubiquitin ligases, including the CRLs, which are activated by neddylation, play an important role in diverse biological processes and are involved in various human diseases, particularly cancer. The book covers various topics, such as CRL structure, biology, genetics, its regulation by neddylation, its pivotal role in human disease, and its potential in drug discovery and targeted therapies. The book appeals to biochemists and biologists working in other fields, and, given the importance of CRLs in all aspects of cell biology and the great promise of targeting these complexes for therapy, is a valuable resource anyone interested in modern biology or medicine.

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.

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 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.

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"

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.

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.

From small beginnings in the early 1970s, the study of complement regulatory proteins has grown in the last decade to the point where it dominates the complement field. This growth has been fueled by the discovery of new regulators, the cloning of old and new regulators, the discovery that many of the regulators are structurally and evolutionarily related to each other and the development of recombinant forms for use in therapy. There are now more proteins known to be involved in controlling the complement system than there are components of the system and the list continues to grow. The time is ripe for a comprehensive review of our current knowledge of these intriguing proteins. This book does just that. The first few chapters discuss the "nuts-and-bolts" of the complement regulators, describing their structures, functional roles and modes of action. The roles of the complement regulators "in vivo" are then described, focusing on the consequences of deficiency, roles in the reproductive system, interactions with pathogens and exploitation for therapy. The interesting developments in defining the complement regulators expressed in other species are also discussed. The book is written as a monograph, albeit by two people. The text is as readable as possible without compromising on scientific accuracy and completeness. The conversational style very evident in some sections is deliberate Placing all references in a single bibliography at the end of the text further improves readability. The reader will go to the book to discover a specific fact but be persuaded to read more and derive pleasure from the process. The authors' enthusiasm for the subject comes over strongly in the text, and this enthusiasm proves infectious.
Key Features
* Complement regulators--structure, functional roles and mode of action
* Comprehensive reviews of each of the individual regulators
* Roles of Complement regulators "in vivo, "in health and disease:
* Consequences of deficiency
* Roles in the reproductive system
* Interactions with pathogens
* Exploitation for therapy
* Complement regulators in other species

This book, a consecutive contribution to the series Challenges and Advances in Computational Chemistry and Physics, focuses on understanding the photoinduced processes in biological systems. Understanding and fine control of light fate in molecules is vital for the progress of society and environmental safety. Light induced changes of various physico-chemical and spectroscopic properties in nucleic acids and proteins is the basis of fundamental biological events such as vision, DNA photodamage or photosensing. The investigation of these processes is challenging to both theoretical and experimental studies. This volume encompasses the quantum mechanics/molecular mechanics theory in several subfields, including: advanced computational methods for nucleic acids and proteins systems; dynamics, spectroscopic and physico-chemical properties of biological photoreceptors; DNA photodamage. This book is of interest to readers in both fundamental and application-oriented research by overviewing recent achievements in computational modeling of excited states in nucleic acids and proteins.

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.

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.

A team of expert investigators and clinical researchers comprehensively review complement's basic biology, its role in disease, methods to measure its activity, and strategies for its inhibition in patients. Each chapter focuses on a specific area of basic and applied complement biology, spelling out the activation pathways and complement receptors. Informative animal models are discussed in detail, including the relative values of each model and the important interspecies differences that can distort the interpretation of preclinical studies. The emphasis throughout is on the pros and cons of the therapeutic use of recombinant complement inhibitors in specific diseases. Cutting-edge and innovative, Therapeutic Interventions in the Complement System highlights for today's researcher and biotechnologist effective strategies of drug discovery and development that are producing valuable new complement inhibitors for the treatment of a wide variety of clinically important diseases.

Protein informatics is a newer name for an already existing discipline. It encompasses the techniques used in bioinformatics and molecular modeling that are related to proteins. While bioinformatics is mainly concerned with the collection, organization, and analysis of biological data, molecular modeling is devoted to representation and manipulation of the structure of proteins.

Protein informatics requires substantial prerequisites on computer science, mathematics, and molecular biology. The approach chosen here, allows a direct and rapid grasp on the subject starting from basic knowledge of algorithm design, calculus, linear algebra, and probability theory.

An Introduction to Protein Informatics, a professional monograph will provide the reader a comprehensive introduction to the field of protein informatics. The text emphasizes mathematical and computational methods to tackle the central problems of alignment, phylogenetic reconstruction, and prediction and sampling of protein structure.

An Introduction to Protein Informatics is designed for a professional audience, composed of researchers and practitioners within bioinformatics, molecular modeling, algorithm design, optimization, and pattern recognition. This book is also suitable as a graduate-level text for students in computer science, mathematics, and biomedicine.

How do you keep track of basic information on the proteins you work with? Where do you find details of their physicochemical properties, amino acid sequences, and structure? Are you tired of scanning review articles, primary papers, and databases to locate that elusive fact?
The Academic Press FactsBook Series has established itself as the best source of easily-accessible and accurate facts about protein groups. Described as "a growing series of excellent manuals" by "Molecular Medicine Today" and "essential works of reference" by "Trends in Biochemical Sciences," the FactsBooks have become the most popular comprehensive data resources available. Using an easy-to-follow format, the FactsBooks will keep you up-to-date with the latest advances in structure, amino acid sequences, physicochemical properties, and biological activity. Meticulously researched and compiled by experts in the field, keeping abreast of developments has never been so easy
The Transporter FactsBook contains entries covering almost 800 transporters. Organized into 55 families of structurally related transporters, this volume includes ATPases, ABC transporters, H+-dependent antiporters and symporters, Na+-dependent antiporters and symporters, and other transporters such as mitochondrial transporters.
Key Features
* Nomenclature, biological sources and substrates
* Phylogenetic relationships
* Predicted structures
* Physical and genetic characteristics
* Multiple amino acid sequence alignments
* Database accession numbers
* Key references

During the course of evolution, an imbalance was created between the rate of vertebrate genetic adaptation and that of the lower forms of living organisms, such as bacteria and viruses. This imbalance has given the latter the advantage of generating, relatively quickly, molecules with unexpected structures and features that carry a threat to vertebrates. To compensate for their weakness, vertebrates have accelerated their own evolutionary processes, not at the level of whole organism, but in specialized cells containing the genes that code for antibody molecules or for T-cell receptors. That is, when an immediate requirement for molecules capable of specific interactions arose, nature has preferred to speed up the mode of Darwinian evolution in pref- ence to any other approach (such as the use of X-ray diffraction studies and computergraphic analysis). Recently, Darwinian rules have been adapted for test tube research, and the concept of selecting molecules having particular characteristics from r- dom pools has been realized in the form of various chemical and biological combinatorial libraries. While working with these libraries, we noticed the interesting fact that when combinatorial libraries of oligopeptides were allowed to interact with different selector proteins, only the actual binding sites of these proteins showed binding properties, whereas the rest of the p- tein surface seemed "inert. " This seemingly common feature of protein- having no extra potential binding sites--was probably selected during evolution in order to minimize nonspecific interactions with the surrounding milieu.

Molecular modeling has undergone a remarkable transformation in the last 20 years. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in the book, along with chapters covering a wide range of subjects. Links to downloadable software are also provided.

Cell membranes are not, as once believed, inert structures designed to contain the cell contents, but are in fact dynamic structures that are as me- bolically active as the cytosol and other cellular compartments they surround. Thus membranes not only contain mixtures of lipid and phospholipids, but also many proteins both embedded deeply within the membrane structure itself and also more loosely attached on the membrane surfaces. Though many such proteins have long been known to act as transport proteins, ion channels, hormone receptors, G proteins, cytoskeletal anchorage points, and so on, the major advance of recent years is the increasing understanding that the lipids and phospholipids in the membrane bilayer itself are also metabolized to b- logically active products that can diffuse either in the cytosol or in the m- brane bilayer to control the function of other proteins. Thus the concept of lipid-derived second messengers is now firmly established.

This book describes the complex structures of heparins and heparan sulfates (heparinoids) and how they are generated by their biosynthetic pathways. The book also details the methodologies for studying these structures and their cellular metabolism. Heparin-Binding Proteins introduces the general nature of interactions between heparinoids and proteins, and presents the role for these structures in their interactions with the proteins of the hemostatic mechanisms, fibroblasts growth factors, superoxide dismutase, and lipoproteins.
Key Features
* Covers cellular metabolism of heparinoid proteoglycans
* Written by a distinguished expert in the field of carbohydrate biochemistry
* Describes the roles of heparan sulfate proteoglycans in
* * Blood coagulation and fibrinolysis
* Lipoprotein metabolism
* Superoxide dismutase activity
* Fibroblast growth factor responses of cells

A readily reproducible collection of established and emerging techniques for studying the interaction between proteins and ligands, including biochemical/bulk techniques, structure analysis, spectroscopy, single-molecule studies, and theoretical/computational tools. Among the highlights are surface plasmon resonance (SPR) and reflectometric biosensor approaches, high-throughput screening with confocal optics microscopy, single molecule fluorescence and fluorescence correlation spectroscopy (FCS), atomic force microscopy (AFM), crystallography of reaction intermediates, and time-resolved x-ray crystallography. The protocols follow the successful Methods in Molecular Biologya"[ series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

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.