The Ras superfamily (>150 human members) encompasses Ras GTPases involved in cell proliferation, Rho GTPases involved in regulating the cytoskeleton, Rab GTPases involved in membrane targeting/fusion and a group of GTPases including Sar1, Arf, Arl and dynamin involved in vesicle budding/fission. These GTPases act as molecular switches and their activities are controlled by a large number of regulatory molecules that affect either GTP loading (guanine nucleotide exchange factors or GEFs) or GTP hydrolysis (GTPase activating proteins or GAPs). In their active state, they interact with a continually increasing, functionally complex array of downstream effectors.
Since the last Methods in Enzymology volume on this topic in 2000, Rho GTPases have continued to receive a huge amount of attention. The human genome sequence has revealed the full extent of the Rho GEF and Rho GAP families (over 80 members for each) and the challenge of identifying the molecular interactions and cellular pathways influenced by each of these regulators is a daunting prospect. This new volume describes some of the methods currently being used to examine Rho family GTPase regulation at the biochemical and cellular level.
*Describes the methods currently being used to examine Rho family GTPase regulation at the biochemical and cellular levels.
*Includes new imaging techniques that revolutionize the ability to visualize GTPase activities.
*Over 150 international contributors.

This edited volume summarizes the recent advancements made in plant science including molecular biology and genome editing , particularly in the development of novel pathways tolerant to climate change-induced stresses such as drought, extreme temperatures, cold, salinity, flooding, etc. These stresses are liable for decrease in yields in many crop plants at global level. Till date conventional plant breeding approaches have resulted in significant improvement of crop plants for producing higher yields during adverse climatic conditions. However, the pace of improvement through conventional plant breeding needs to be accelerated in keeping with the growing demand of food and increasing human populationl, particularly in developing world. This book serves as a comprehensive reference material for researchers, teachers, and students involved in climate change-related abiotic stress tolerance studies in plants.

Intrinsically Disordered Proteins: Dynamics, Binding, and Function thoroughly examines and ties together the fundamental biochemical functions of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs), including signaling, binding, and regulation, with the methodology for study and the associated pathways for drug design and therapeutic intervention. The role of new mechanistic, computational, and experimental approaches in IDP study are explored in depth, with methods for the characterization of IDP dynamics; models, simulations, and mechanisms of IDP and IDR binding; and biological and medical implications of IDP dynamics prominently featured. Written and edited by leading scientists in the field, this book explores groundbreaking areas such as ensemble descriptions of IDPs and IDRs, single-molecule studies of IDPs and IDRs, IDPs and IDRs in membraneless organelles, and molecular mechanisms of fibrillation of IDPs. Intrinsically Disordered Proteins provides students and researchers in biochemistry, molecular biology, and applied microbiology with a comprehensive and updated discussion of the complex dynamics of IDPs and IDRs.

This detailed volume compiles state-of-the-art protocols that will serve as recipes for scientists researching collagen, an abundant protein with great importance to health and disease, as well as in applications like food, cosmetics, pharmaceuticals, cosmetic surgery, artificial skin, and glue. Beginning with a section on in vitro models for the characterization of collagen formation, the book continues by highlighting large-scale analysis of collagen with mass spectrometry in order to elucidate the proteomics, degradomics, interactomes, and cross-linking of collagen, high resolution imaging approaches for collagen by the use of scanning electron microscopy and multiphoton imaging, as well as the role of collagen during physiological and pathological conditions. Written for the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Collagen: Methods and Protocols is an ideal guide to high quality and repeatable protocols in this vital field of study.

This volume brings together a plethora of protocols and experimental methods used by scientists to study calpains, their inhibitors, and their substrates. It also explores bioinformatic approaches to calpain substrate identification. The chapters in this book are divided into five parts and cover topics such as production and purification of calpains; determination of calpain localization, expression, and activity; identification of calpain-activated protein function; interrogation of calpastatin; and manipulation of calpain expression. 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. Cutting-edge and practical, Calpain: Methods and Protocols is a valuable resource for researchers and scientists who want to learn more about this developing field, and get inspired to make new discoveries that will aid in diagnosing and treating calpain-related diseases.

An accompanying volume (Volume 6) in this series presents strategies of cellular invasion from the viewpoint of the microbe.
This filed of study is growing rapidly after a somewhat slow start over recent decades. This collection of invited chapters attempts to reflect current research, and brings together cell biologists, microbiologists and immunologists with disparate interests. However, there is a certain unity, even repetition of key themes, hopefully like a symphony rather than a boring catalogue. It will be evident that editorial bias favors intracellular paratism and medically important organisms. The neutrophil is far more than a supporting player to the macrophage, and some attempt is made to remind the reader of some of its unique skills. To retain a manageable size, the emphasis is on relatively early events such as mutual recognition, cell entry, and response, rather than on longterm changes in gene expression by either host cell or pathogen. Viruses are excluded not because of lack of importance but because of somewhat different research approaches, although it is cytogenes, share common strategies in invasion and intercellular spread.

This book reviews the advances and challenges of structure-based drug design in the preclinical drug discovery process, addressing various diseases, including malaria, tuberculosis and cancer. Written by internationally recognized researchers, this edited book discusses how the application of the various in-silico techniques, such as molecular docking, virtual screening, pharmacophore modeling, molecular dynamics simulations, and residue interaction networks offers insights into pharmacologically active novel molecular entities. It presents a clear concept of the molecular mechanism of different drug targets and explores methods to help understand drug resistance. In addition, it includes chapters dedicated to natural-product- derived medicines, combinatorial drug discovery, the CryoEM technique for structure-based drug design and big data in drug discovery. The book offers an invaluable resource for graduate and postgraduate students, as well as for researchers in academic and industrial laboratories working in the areas of chemoinformatics, medicinal and pharmaceutical chemistry and pharmacoinformatics.

Protein-Protein Interactions in Human Disease, Volume 111, Part B, promotes further research and development in the protein interaction network in order to identify critical proteins involved in the etiology of human diseases and locate new protein targets for drug development. Thus, this volume is of considerable interest to protein chemists, pharmacologists, cell biologists, immunologists, structural biologists, computational biochemists and other researchers working in the field. In addition, these articles would be of great benefit to medical, biology and pharmacology students who specialize in this field.

This volume explores the latest methods used to study AMPK by computational, biochemical, biophysical, cellular, and ex vivo and in vivo approaches. The chapters in this book cover specific topics, such as methods to measure change in cellular energy metabolism and analyze metabolic pathways regulated by AMPK; bioinformatics tools to identify AMPK targets; knockdown of AMPK by CRISPR-Cas9; production and crystallization of full-length human AMP-activated protein kinase; cell-free assays to measure the effects of regulatory ligands on AMPK; use of sensors of AMPK activity; AMPK protein interaction by yeast two-hybrid; the role of AMPK in inflammation and autophagy; analyzing the AMPK function in C. elegans and mammals (with special focus on skeletal muscle, blood vessels, kidneys, pancreatic islets and hypothalamus); and human 2 AMPK mutations. 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. Cutting edge and thorough, AMPK: Methods and Protocols is a valuable resource for graduate students, postdoctoral researchers, and established investigators who are interested in the richly diverse AMPK field.

This book focuses on the regulation of transcription and translation in Archaea and arising insights into the evolution of RNA processing pathways. From synthesis to degradation and the implications of gene expression, it presents the current state of knowledge on archaeal RNA biology in 13 chapters. Topics covered include the modification and maturation of RNAs, the function of small non-coding RNAs and the CRISPR-Cas defense system. While Archaea have long been considered exotic microbial extremophiles, they are now increasingly being recognized as important model microorganisms for the study of molecular mechanisms conserved across the three domains of life, and with regard to the relevance of similarities and differences to eukaryotes and bacteria. This unique book offers a valuable resource for all readers interested in the regulation of gene expression in Archaea and RNA metabolism in general.

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 highlights the role of the Translationally Controlled Tumor Protein (TCTP) in cell signaling, cell fate and the resulting connection to disease development. It begins by discussing the structure/function of TCTP, before exploring its role in different species ranging from plants to Drosophila and covering fields such as development, the cytoskeleton, cell division, DNA fragility and apoptosis. In turn, the book's final section is devoted to the role of TCTP in disease, namely asthma and diverse cancers, and ultimately as a target for the treatment of malignancies. What is the common denominator between all these processes and why is TCTP necessary in order for them to occur, even in the worst case such as cancer? The book seeks to provide meaningful answers to this and other key questions. Presenting a broad and revealing view on the topic, it offers an informative guide for scientists and students alike.

This book provides a timely state-of-the-art overview of voltage-gated sodium channels, their structure-function, their pharmacology and related diseases. Among the topics discussed are the structural basis of Na+ channel function, methodological advances in the study of Na+ channels, their pathophysiology and drugs and toxins interactions with these channels and their associated channelopathies.

G Protein Coupled Receptors, Second Edition, Volume 143, a new volume in the Methods in Cell Biology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. It contains a wide array of topics about the G protein coupled receptors, as well as updates of chapters from the first edition.

Neuropeptide Y (NPY) is a ubiquitous and important messenger in the nervous system, with a wide range of physiological roles. It is involved in the body energy balance and is one of the most potent stimuli of food intake known. NPY also acts to regulate central and peripheral autonomic functions.
This book, written by academic and industrial experts in the field, links the most recent basic experimental knowledge about NPY and its receptors with areas of clinical importance.
This book will be of interest to those working in all areas of research affected by NPY, such as food intake and energy homeostasis, cardiovascular regulation and G-protein-coupled receptors, as well as those interested in the development of drugs as NPY targets.
Key Features
* The hypothalamic role of NPY and its relationship with eating disorders and diabetes
* The sympathetic nervous system role of NPY and its involvement in cardiovascular disorders
* Characterization of NPY receptor types and their brain distribution, molecular biology and pharmacology
* Development of peptide and non-peptide receptor antagonists

In this book, renowned scientists describe the role of steroid chirality and modification of lipid membrane physical properties in the modulation of G protein-coupled receptors and ion channels. The application of commonly-used technical approaches such as mass spectrometry and nucleic magnetic resonance transfer spectroscopy for studies on cholesterol distribution and alteration of lipid bilayer characteristics is also discussed. This book offers comprehensive insights into the current understanding of cholesterol-driven modulation of protein function via mechanisms that extend beyond lipid-protein direct interactions. In the first part, the chapters introduce the reader to the use of the chemical derivatives of cholesterol as a valuable laboratory tool in the studies of cholesterol-driven modulation of protein function. In the second part, examples of cholesterol-induced changes in membrane physical characteristics are presented and discussed in light of their multifaceted contribution to the effect of cholesterol on protein function. The book will be of interest to undergraduate and graduate students as well as basic science and medical researchers with a keen interest in the biophysical properties of cholesterol and physiological consequences of cholesterol presence in biological systems.

The elucidation during the latter half of the 20th century of the mechanisms by which information flows from nucleic acids to proteins has completely changed the face of biological research. Many diseases are caused by abnormalities in control mechanisms which are not immediately essential for life itself but which maintain the normal social behavior of differentiated cells in multicellular organisms. The complex sugar chains of glycoproteins and glycolipids are believed to play important roles in the control of cellular functions and in recognition between the cell and its cellular and fluid environment. Investigations into the abnormalities of complex sugar chain assembly are expected to yield an important new underatanding of the etiology and pathogenesis of human diseases. This volume discusses several representative diseases which emphasize the current status of glycopathology, and will stimulate further research in this exciting field.

This volume is a wide-ranging tool for studying protein-carbohydrate interactions that extend from traditional biochemical methods to state-of-the-art techniques. This book focuses on four different research themes: Part I describes methods for screening and quantifying CAZyme activity; Part II contains methods for investigating the interactions between proteins and carbohydrate ligands; Part III discusses methods for the visualization of carbohydrates and protein-carbohydrate complexes; and Part IV focuses on structural and "omic" approaches for studying systems of CAZymes. 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. Cutting-edge and thorough, Protein-Carbohydrate Interactions: Methods and Protocols is a valuable resource to the glycomics research community. In this continuously advancing field, the methods in this book highlight the biology of glycomics, thus driving biotechnological innovation and solutions for human health and sustainable resources within the emerging green community.

This volume covers an array of techniques available for studying peptide-protein docking and design. The book is divided into four sections: peptide binding site prediction; peptide-protein docking; prediction and design of peptide binding specificity; and the design of inhibitory peptides. The chapters in Modeling Peptide-Protein Interactions: Methods and Protocols cover topics such as the usage of ACCLUSTER and PeptiMap for peptide binding site prediction; AnchorDock and ATTRACT for blind, flexible docking of peptides to proteins; flexible peptide docking using HADDOCK and FlexPepDock; identifying loop-mediated protein-protein interactions using LoopFinder; and protein-peptide interaction design using PinaColada. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary details for successful application of the different approaches and step-by-step, readily reproducible protocols, as well as tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Modeling Peptide-Protein Interactions: Methods and Protocols provides a diverse and unified overview of this rapidly advancing field of major interest and applicability.

This volume takes a closer look how the cell organelles Golgi apparatus (also known as the Golgi complex or Golgi body), and centriole are structurally and functionally intertwined. Initially, it was believed that the role of Golgi complex is limited to the packaging and preparation for secretion of various cellular proteins, while the centriole participates in cell division and cilia formation. However, since their discovery nearly 200 years ago, it became clear that these two organelles are interacting, and that their functions are much more complex and far reaching than previously thought. Recent findings indicate that the Golgi-Centriole relationship may be important for directional protein transport, cell polarization and cell cycle progression. Current studies indicate that Golgi and centriole also participate in development and act as cellular and immunological sensors, and that their abnormalities lead to cell and developmental abnormalities, Alzheimer, cancer, various lipid disorders and neurological and immunological diseases in humans. This volume combines the latest information on the structure, molecular composition, and roles of Golgi and centriole in various cellular functions and diseases. The better understanding of the Golgi-centriole interactions may lead to the development of novel therapies for the treatment of various diseases, including cancer.

This book presents multiple new and classical methods for studying the vital poly-ADP-ribose (pADPr) pathway. Beginning with techniques for the detection and quantification of the product of poly(ADP-ribose) polymerase (PARP) enzymatic activity and detection of variation in pADPr production during the cell cycle, the volume continues with sections on the identification of pADPr protein acceptors, methods focusing on studying molecular mechanisms of PARP functions in eukaryotic cells, particularly those involved in control of DNA repair and oxidative stress, as well as in expression regulation, approaches to the in vitro reconstitution of PARP-1 interaction with chromatin, the development and testing of small molecule PARP inhibitors, and the functions of understudied members of PARP family. Written for the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Poly(ADP-Ribose) Polymerase: Methods and Protocols, Second Edition serves as an ideal companion to the first edition for scientists whose investigations involve this important pathway. The chapter 'Identifying and Validating Tankyrase Binders and Substrates: A Candidate Approach' is published open access under a CC BY 4.0 license.

An in-depth look at the latest research, methods, and applications in the field of protein bioinformatics This book presents the latest developments in protein bioinformatics, introducing for the first time cutting-edge research results alongside novel algorithmic and AI methods for the analysis of protein data. In one complete, self-contained volume, Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics addresses key challenges facing both computer scientists and biologists, arming readers with tools and techniques for analyzing and interpreting protein data and solving a variety of biological problems. Featuring a collection of authoritative articles by leaders in the field, this work focuses on the analysis of protein sequences, structures, and interaction networks using both traditional algorithms and AI methods. It also examines, in great detail, data preparation, simulation, experiments, evaluation methods, and applications. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics: * Highlights protein analysis applications such as protein-related drug activity comparison * Incorporates salient case studies illustrating how to apply the methods outlined in the book * Tackles the complex relationship between proteins from a systems biology point of view * Relates the topic to other emerging technologies such as data mining and visualization * Includes many tables and illustrations demonstrating concepts and performance figures Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics is an essential reference for bioinformatics specialists in research and industry, and for anyone wishing to better understand the rich field of protein bioinformatics.

This thesis focuses on the study of interactions between protein and peptides and their potential applications in cell imaging and nanoparticle surface modification. Drawing inspiration from naturally occurring coiled-coil binding pairs, it proposes a novel covalent peptide tag and probe system, based on the concept of "affinity guided covalent conjugation." This newly established methodology provides complementary resolution to protein labeling, imaging and trafficking. By systematically investigating the coordination interaction between protein and quantum dots using various engineered protein ligands, this thesis proposes a general rule for protein self-assembly on the surface of quantum dots and reports a revolutionized nanobelt protein in accordance with this rule. It is an extraordinary example of interdisciplinary research, providing answers to real-life biological problems from a chemistry perspective.

Part I covers modern advances in the determination of
glycoprotein structure and in the biosynthesis of mammalian,
bacterial, yeast, plant and insect glycoproteins. There are also
two chapters on functional aspects (glycoprotein hormones and
collagens).
The content of the volume is very comprehensive in that, most
contributors have focussed on discussing, in depth, the wealth
of most recent advances in their field, and referring to previous
reviews of older work for background information. This method can
effectively produce a very wide subject coverage in a smaller
number of chapters/volumes. The volume is an important
information source for all glycobiologist researchers (senior
investigators, post-doctoral fellows and graduate students), and
as a good, comprehensive, reference text for scientists working in
the life sciences.