Intermediate filaments are a large family of proteins that are the cytoskeletal elements involved in a number of skin, liver, neuromuscular, cardiac, eye and hair diseases. Intermediate filament genes are regulated in a tissue-and cell type-specific manner and their polymerized protein products protects the cells and tissue they are part of against a variety of mechanical and nonmechanical stresses. This book provides a comprehensive resource of methodology essentials, describing a variety of essential tools and assays for studying intermediate filaments. The book provides user-friendly advice and protocols covering all aspects of intermediate filaments including protein isolation and structure, protein and gene regulation, relationship to disease and apoptosis, and associated proteins. Both mammalian and non-mammalian systems and animal models are covered, making this book a must-have for any investigator wishing to study IF genes or their protein products.
* Covers intermediate filaments from crystallography, protein chemistry, cell and molecular biology, microrheology, gene regulation, to animal models and human disease
* Practical and user-friendly with detailed "how-to-protocols and "tricks of the trade"
* Includes detailed tables of useful reagents, vendors and web links

This book reflects more than three decades of research on Cellular Automata (CA), and nearly a decade of work on the application of CA to model biological strings, which forms the foundation of 'A New Kind of Computational Biology' pioneered by the start-up, CARLBio. After a brief introduction on Cellular Automata (CA) theory and functional biology, it reports on the modeling of basic biological strings with CA, starting with the basic nucleotides leading to codon and anti-codon CA models. It derives a more involved CA model of DNA, RNA, the entire translation process for amino acid formation and the evolution of protein to its unique structure and function. In subsequent chapters the interaction of Proteins with other bio-molecules is also modeled. The only prior knowledge assumed necessary is an undergraduate knowledge of computer programming and biology. The book adopts a hands-on, "do-it-yourself" approach to enable readers to apply the method provided to derive the CA rules and comprehend how these are related to the physical 'rules' observed in biology. In a single framework, the authors have presented two branches of science - Computation and Biology. Instead of rigorous molecular dynamics modeling, which the authors describe as a Bottoms-Up model, or relying on the Top-Down new age Artificial Intelligence (AI) and Machine Language (ML) that depends on extensive availability of quality data, this book takes the best from both the Top-Down and Bottoms-up approaches and establishes how the behavior of complex molecules is represented in CA. The CA rules are derived from the basic knowledge of molecular interaction and construction observed in biological world but mapped to a few subset of known results to derive and predict results. This book is useful for students, researchers and industry practitioners who want to explore modeling and simulation of the physical world complex systems from a different perspective. It raises the inevitable the question - 'Are life and the universe nothing but a collection of continuous systems processing information'.

Experts from around the world review the current field of the immunobiology of heat shock proteins, and provide a comprehensive account of how these molecules are spearheading efforts in the understanding of various pathways of the immune system. This one-stop resource contains numerous images to both help illustrate the research on heat shock proteins, and better clarify the field for the non-expert. Heat shock proteins (HSPs) were discovered in 1962 and were quickly recognized for their role in protecting cells from stress. Twenty years later, the immunogenicity of a select few HSPs was described, and for the past 30 years, these findings have been applied to numerous branches of immunology, including tumor immunology and immunosurveillance, immunotherapy, etiology of autoimmunity, immunotherapy of infectious diseases, and expression of innate receptors. While HSPs can be used to manipulate immune responses by exogenous administration, they appear to be involved in initiation of de novo immune responses to cancer and likely in the maintenance of immune homeostasis.

Poly (ADP-ribose) Polymerases (PARPs) are abundant and ubiquitous proteins that regulate crucial processes of the cell cycle, DNA repair, genomic stability, and transcriptional regulation. Being involved in basic cell functions, PARPs mediate rapid responses to such environmental factors as stress, infection, nutrition and hormonal signals. Whereas PARP inhibitors can suppress tumor growth and proliferation in certain breast, ovarian, and prostate cancers, understanding how PARP controls cellular functions is essential for the development of novel cancer treatments strategies. Divided into three convenient sections, Poly(ADP-Ribose) Polymerase: Methods and Protocols aims to explain how PARP proteins act within the normal development of an organism as well as in pathogenic conditions, seeks to advance the knowledge of developmental pathways regulation, and endeavors to facilitate the development of new therapeutic drugs and methods to target PARP-dependent processes. 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, Poly(ADP-Ribose) Polymerase: Methods and Protocols serves as an ideal guide to scientists who wish to continue exploring this exciting and progressive research field.

This volume aims to provide protocols on a wide range of biochemical methods, analytical approaches, and bioinformatics tools developed to analyze the proteome. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Proteomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Genetics of Prion Disease, by S. Lloyd, S. Mead and J. Collinge. Atypical Prion Diseases in Humans and Animals, by M. A. Tranulis, S. L. Benestad, T. Baron and H. Kretzschmar. Chronic Wasting Disease, by S. Gilch, N. Chitoor, Y. Taguchi, M. Stuart, J. E. Jewell and H. M. Schatzl. Transgenic Mouse Models and Prion Strains, by G. C. Telling. Neuroprotective and Neurotoxic Signaling by the Prion Protein, by U. K. Resenberger, K. F. Winklhofer and J. Tatzelt. Prion Seeded Conversion and Amplification Assays, by C. D. Orru and B. Caughey. Prion Protein and Its Conformational Conversion: A Structural Perspective, by W. K. Surewicz and M. I. Apostol. Molecular Dynamics as an Approach to Study Prion Protein Misfolding and the Effect of Pathogenic Mutations, by M.W. van der Kamp and V. Daggett. Chemical Biology of Prion Protein: Tools to Bridge the In Vitro/Vivo Interface, by R. Seidel and M. Engelhard. The PrP-Like Proteins Shadoo and Doppel, by D. Westaway, N. Daude, S. Wohlgemuth and P. Harrison. Fungal Prions: Structure, Function and Propagation, by M. F. Tuite, R. Marchante and V. Kushnirov."

Michael D. Wendt
Protein-Protein Interactions as Drug Targets

Shaomeng Wang, Yujun Zhao, Denzil Bernard, Angelo Aguilar, Sanjeev Kumar
Targeting the MDM2-p53 Protein-Protein Interaction for New Cancer Therapeutics

Kurt Deshayes, Jeremy Murray, Domagoj Vucic
The Development of Small-Molecule IAP Antagonists for the Treatment of Cancer

John F. Kadow, David R. Langley, Nicholas A. Meanwell, Michael A. Walker, Kap-Sun Yeung, Richard Pracitto
Protein-Protein Interaction Targets to Inhibit HIV-1 Infection
Nicholas A. Meanwell, David R. Langley
Inhibitors of Protein-Protein Interactions in Paramyxovirus Fusion a Focus on Respiratory Syncytial Virus

Andrew B. Mahon, Stephen E. Miller, Stephen T. Joy, Paramjit S. Arora
Rational Design Strategies for Developing Synthetic Inhibitors of Helical Protein Interfaces

Michael D. Wendt
The Discovery of Navitoclax, a Bcl-2 Family Inhibitor

"

Receptor Tyrosine Kinase: Structure, Functions and Role in Human Disease, for the first time, systematically covers the shared structural and functional features of the RTK family. Receptor Tyrosine Kinases (RTKs) play critical roles in embryogenesis, normal physiology and several diseases. And over the last decade they have become the Number 1 targets of cancer drugs. To be able to conduct fundamental research or to attempt to develop pharmacological agents able to enhance or intercept them, it is essential first to understand the evolutionary origin of the 58 RTKs and their roles in invertebrates and in humans, as well as downstream signaling pathways. The assembly of chapters is written by experts and underscores commonalities between and among the RTKs. It is an ideal companion volume to The Receptor Tyrosine Kinase: Families and Subfamilies, which proceeds, family by family through all of the specific subfamilies of RTKs, along with their unique landmarks.

This book presents modern and classic analytical approaches that are crucial for the biochemical and functional characterization of the archetypal protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The distinguishing feature of the book is that it covers, in addition to other methods, some of the uncommon but valuable techniques as well. For example, in-gel visualization of enzyme activity, immunoblotting protocols for native (non-denatured) proteins, and proteins resolved by pH-gradient [IEF-isoelectrofocusing], etc. These expedient methods are relevant and vital for the verification of biochemical properties of GAPDH, or similar protein of interest. This work outlines detailed protocols that are essential to investigate classical (cellular) and recently reported extracellular (secretory) isoforms of GAPDH. Precisely, the book covers techniques pertinent to enzymatic and non-enzymatic analysis of GAPDH that include, but not limited to, electrophoretic mobility shift assay (EMSA), two-dimensional (2D)-immunoblotting, immunofluorescence/confocal microscopy, mass spectrometry, ion-exchange and affinity chromatography. Readers will discover the importance of the experimental methods described in the book as they relate to the evaluation of the role and significance of GAPDH. Furthermore, majority of the methods described in the book have also been validated in the author's laboratory, besides other research groups worldwide, underlining the repeatability and reproducibility of the protocols. Each method begins with an abstract and a brief background emphasizing its application and relevance. This will enable the readers to determine the choice of experimental design according to their research objectives. The book explains the methods systematically with ample illustrations to facilitate quick and easy comprehension of the practical knowledge. Although the book is focused on GAPDH, many of the protocols may be adopted to other proteins or enzymes with minimal modifications. Noteworthy, it is unequivocally established that GAPDH is a multifunctional protein involved in several cellular processes of health & disease conditions. Hence, this book will be a valuable practical guide for young researchers, scientists and clinician-scientists.

This work establishes linear-scaling density-functional theory (DFT) as a powerful tool for understanding enzyme catalysis, one that can complement quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics simulations. The thesis reviews benchmark studies demonstrating techniques capable of simulating entire enzymes at the ab initio quantum-mechanical level of accuracy. DFT has transformed the physical sciences by allowing researchers to perform parameter-free quantum-mechanical calculations to predict a broad range of physical and chemical properties of materials. In principle, similar methods could be applied to biological problems. However, even the simplest biological systems contain many thousands of atoms and are characterized by extremely complex configuration spaces associated with a vast number of degrees of freedom. The development of linear-scaling density-functional codes makes biological molecules accessible to quantum-mechanical calculation, but has yet to resolve the complexity of the phase space. Furthermore, these calculations on systems containing up to 2,000 atoms can capture contributions to the energy that are not accounted for in QM/MM methods (for which the Nobel prize in Chemistry was awarded in 2013) and the results presented here reveal profound shortcomings in said methods.

This book provides coverage, methodology, and laboratory protocols on the more essential aspects of protein tyrosine phosphatase (PTP) function and regulation, including the use of standardized in vitro functional assays, suitable cell systems, and animal and microorganism models. Chapters covering state-of-the-art technical approaches suitable to decipher the physiologic roles of PTPs, and their involvement in tissue-specific functions, are also included, which will be of utility for both newcomers and experienced researchers in the field of tyrosine- and phosphoinositide- phosphorylation/dephosphorylation. 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 practical, Protein Tyrosine Phosphatases: Methods and Protocols aims to aid researchers in better defining the common and individual features of the PTP family members and translating this knowledge into PTP-based therapy for human disease.

Blood science has become a cornerstone of multiple disciplines, including clinical chemistry, disease diagnosis, and therapeutic monitoring. Over the past decade, we have witnessed the advent of increasingly powerful proteomics technologies that allow greater fundamental insights into the blood proteome. These technological improvements have, in part, fuelled the quest for the discovery of novel blood-based biomarkers of disease. Serum/Plasma Proteomics: Methods and Protocols is a comprehensive resource of protocols for areas, pre-analytical through to analytical, of plasma and serum proteomics. Divided into five convenient sections, this detailed volume covers fractionation strategies for in-depth blood proteome analysis, defined procedures for blood collection, handling and storage, detailed protocols for performing both antibody-based and non-antibody based quantitative assays, proteome analysis of blood cell compartments, circulating nanomebraneous vesicles and blood-related fluids, and finally data management, statistical design, and bioinformatic challenges. This book, contributed to by leading experts in the field, provides a valuable foundation for the development and application of blood-based proteomics. 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 easily accessible, Serum/Plasma Proteomics: Methods and Protocols, with its well-honed methodologies, seeks to serve both professionals and investigators new to the field in an effort to further our knowledge of this fundamental science.

In one volume this book provides useful and innovative protocols developed specifically for the proteomic profiling of human tissues. The book provides high-throughput gel-based techniques, microarrays and a number of other methods used in proteomic research. This important book will prove indispensable to investigators of biomarker discovery and therapeutic response profiling, as well as those forging new paths in the fields of theranostics and personalized medicine.

Recent major advances in our understanding of modulating protein functions has led to the development of new methods and algorithms to predict and decipher how amino acid sequences shape three-dimensional structures. Protein Design: Methods and Applications presents the most up-to-date protein design and engineering strategies so that readers can undertake their own projects with a maximum chance of success.
The authors present integrated computational approaches that require various degrees of computational complexity, and the major accomplishments that have been achieved in the design and structural characterization of helical peptides and proteins. Other topics of discussion include: design of structural elementary motifs, entire proteins, and interfaces of protein complexes, and of amyloidogenic polypeptides and amyloid inhibitors.
Authoritative and cutting-edge, Protein Design: Methods and Applications will be of major interest to protein scientists, biochemists, and all experimentalists selecting the strategy most adaptable for their design problem.

Protein Transcription is a key element of cellular and organ regulation. This volume covers structure and function of all major elements associated with transcription.
*Mechanism of RNA polymerase I Transcription
*Structure and function of RNA Polymerase II
*Structure and function of the TFIID complex
*Functional properties of Chromatin Remodeling Enzymes
*Posttranslational modification

This book offers an overview of our current understanding of host defense peptides and their potential for clinical applications as well as some of the obstacles to this. The chapters, written by leading experts in the field, detail the number and diversity of host defense peptides, and discuss the therapeutic potential not only of antibacterial, but also of antifungal, antiviral, plant antimicrobial and anticancer host defense peptides. The authors provide new insights into their mechanisms of action and their immunomodulatory properties, and review recent advances in the design of novel therapeutic molecules. Lastly, their potential to prevent preterm births and Staphylococcus aureus infections is highlighted. The book is of interest to researchers, industry and clinicians alike.

The work reported in this book represents an excellent example of how creative experimentation and technology development, complemented by computational data analysis, can yield important insights that further our understanding of biological entities from a systems perspective. The book describes how the study of a single RNA-binding protein and its interaction sites led to the development of the novel 'protein occupancy profiling' technology that for the first time captured the mRNA sequence space contacted by the ensemble of expressed RNA binders. Application of protein occupancy profiling to eukaryotic cells revealed that extensive sequence stretches in 3' UTRs can be contacted by RBPs and that evolutionary conservation as well as negative selection act on protein-RNA contact sites, suggesting functional importance. Comparative analysis of the RBP-bound sequence space has the potential to unravel putative cis-acting RNA elements without a priori knowledge of the bound regulators. Here, Dr. Munschauer provides a comprehensive introduction to the field of post-transcriptional gene regulation, examines state-of-the-art technologies, and combines the conclusions from several journal articles into a coherent and logical story from the frontiers of systems-biology inspired life science. This thesis, submitted to the Department of Biology, Chemistry and Pharmacy at Freie Universitat Berlin, was selected as outstanding work by the Berlin Institute for Medical Systems Biology at the Max-Delbrueck Center for Molecular Medicine, Germany.

Nuclear G-Protein Coupled Receptors: Methods and Protocols is a compilation of a number of conceptual and methodological aspects important for the validation and characterization of intacrine signaling systems. To date, the best-characterized intracrine signaling system is that of angiotensin II (Ang II), covered in depth in various chapters. Methodology to study the subcellular localization and function of GPCRs and other signaling systems is provided, as well as numerous chapters focusing on methods designed to understand signaling mediated by nuclear and other internal GPCRs. Methods are also described to study the formation of second messengers such as cAMP and to study the trafficking of receptors from the cell surface. 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, Nuclear G-Protein Coupled Receptors: Methods and Protocols seeks to serve both professionals and novices with state-of-the-art approaches to characterize what is becoming a common theme in cellular signaling.

The multidisciplinary science of chemical proteomics studies how small molecules of synthetic or natural origin bind to proteins and modulate their function. In Chemical Proteomics: Methods and Protocols, expert researchers in the field provide key techniques to investigate chemical proteomics focusing on analytical strategies, how probes are generated, techniques for the discovery of small molecule targets and the probing of target function, and small molecule ligand and drug discovery. 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, Chemical Proteomics : Methods and Protocols seeks to provide methodologies that will contribute to a wider application of chemical proteomics methods in biochemical and cell biological laboratories.

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.

Artificial riboswitches and other ligand-responsive gene regulators make it possible to switch protein synthesis ON or OFF with arbitrary ligand molecules. Artificial Riboswitches: Methods and Protocols focuses on the state-of-the-art methods developed in recent years for creating artificial riboswitches, therefore this volume could be regarded as a collection of recipes for the gene circuit elements in synthetic biology and metabolic engineering. Chapters cover topics such as screening or rational design methods for obtaining artificial riboswitches that function in either bacterial or eukaryotic translational systems, protocols for evaluating the activities of the resultant riboswitches, as well as protocols for construction of ligand-dependent, trans-acting gene regulators. 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, Artificial Riboswitches: Methods and Protocols seeks to serve not only bioengineers who aim to reprogram cell behaviors and molecular biologists who leverage these regulators for genetic studies, but to all researchers interested in this fascinating field.

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.

Echinostomes are medically- and veterinary-important parasitic flatworms that invade humans, domestic animals and wildlife and also parasitize in their larval stages numerous invertebrate and cold-blooded vertebrate hosts. The interest in echinostomes in parasitology and general biology comes from several areas: (1) Human infections; (2) Experimental models; (3) Animal infections; (4) Systematics. The application of novel techniques is moving the echinostomes to the frontline of parasitology in fields such as systematics, immunobiology in vertebrate and invertebrate organisms and proteomics among others. The Biology of Echinostomes demonstrates the application of new techniques to a group of trematodes that may serve to obtain information of great value in parasitology and general biology. The book includes basic topics, such as biology and systematics, as well as more novel topics, such as immunobiology, proteomics, and genomics of echinostomes. The authors of each chapter emphasize their content with: (i) the most novel information obtained; (ii) analysis of this information in a more general context (i.e. general parasitology); and (iii) future perspectives in view of the information presented. The subjects are analyzed from a modern point of view, considering aspects such as applications of novel techniques and an analysis of host-parasite interactions.

"Directed Evolution Library Creation: Methods and Protocols, Second Edition "presents user-friendly protocols for both proven strategies and cutting-edge approaches for the creation of mutant gene libraries for directed evolution. As well as experimental methods, information on current computational approaches is provided in a user-friendly format that will allow researchers to make informed choices without needing to comprehend the full technical details of each algorithm. Directed evolution has become a fundamental approach for engineering proteins to enhance activity and explore structure-function relationships, and has supported the rapid development of the field of synthetic biology over the last decade. Divided into three convenient sections, topics include point mutagenesis strategies, recombinatorial methods wherein genetic diversity is sourced from multiple parental genes that are combined via either homology-dependent or -independent techniques and a variety of computational methods to guide the design and analysis of mutant libraries. 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, "Directed Evolution Library Creation: Methods and Protocols, Second Edition "will serve as a reliable manual for both novice and experienced protein engineers and synthetic biologists and will enable further technical innovation and the exploitation of directed evolution for a deeper understanding of protein design and function.

This volume describes protocols for basic state-of-the-art approaches in the field of peptidomics. Most of these approaches are independent of the instruments used for analysis and can easily be adapted for equipment that is available in a typical proteomics facility. Chapters detail many of the basic techniques used to detect and identify peptides, methods for the relative quantitation of peptides between samples using isotopic labels or label-free approaches, and biological species as well as sample types. Written in the highly successful format of the Methods in Molecular Biology series, each chapter includes an introduction to the topic, a list of the necessary materials and reagents, reproducible step-by-step laboratory protocols, and tips on troubleshooting common problems and avoiding pitfalls. Authoritative and practical, Peptidomics: Methods and Strategies provides useful guidance for studies in the rapidly growing field of peptidomics.