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 presents established bioinformatics tools and databases for function prediction of proteins. Reflecting the diversity of this active field in bioinformatics, the chapters in this book discuss a variety of tools and resources such as sequence-, structure-, systems-, and interaction-based function prediction methods, tools for functional analysis of metagenomics data, detecting moonlighting-proteins, sub-cellular localization prediction, and pathway and comparative genomics databases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step instructions of how to use software and web resources, use cases, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Protein Function Prediction: Methods and Protocols is a valuable and practical guide for using bioinformatics tools for investigating protein function

This volume serves as a valuable handbook for the development of nanomedicines made of polymer nanoparticles because it provides researchers, students, and entrepreneurs with all the material necessary to begin their own projects in this field. Readers will find protocols to prepare polymer nanoparticles using different methods, since these are based on the variety of experiences that experts encounter in the field. In addition, complex topics such as, the optimal characterization of polymer nanoparticles is discussed, as well as practical guidelines on how to formulate polymer nanoparticles into nanomedicines, and how to modify the properties of nanoparticles to give them the different functionalities required to become an efficient nanomedicine for different clinical applications. The book also discusses the translation of technology from research to practice, considering aspects related to industrialization of preparation and aspects of regulatory and clinical development.

This two-volume set takes an in-depth look at stress signaling in plants from a uniquely genomic and proteomic perspective and offers a comprehensive treatise that covers all of the signaling pathways and mechanisms that have been researched so far. Currently, plant diseases, extreme weather caused by climate change, drought and an increase in metals in soil are amongst the major limiting factors of crop production worldwide. They devastate not only the food supply but also the economy of a nation. With global food scarcity in mind, there is an urgent need to develop crop plants with increased stress tolerance so as to meet the global food demands and to preserve the quality of our planet. In order to do this, it is necessary to understand how plants react and adapt to stress from the genomic and proteomic perspective. Plants adapt to stress conditions by activating cascades of molecular mechanisms, which result in alterations in gene expression and synthesis of protective proteins. From the perception of the stimulus to the transduction of the signal, followed by an appropriate cellular response, the plants employ a complex network of primary and secondary messenger molecules. Cells exercise a large number of noticeably distinct signaling pathways to regulate their activity. In order to contend with different environmental adversities, plants have developed a series of mechanisms at the physiological, cellular and molecular levels that respond to stress. Each chapter in this volume provides an in-depth explanation of what we currently know of a particular aspect of stress signaling and where we are heading. Together with the highly successful first volume, Stress Signaling in Plants: Genomics and Proteomics Perspective, Volume 2 covers an important aspect of plant biology for both students and seasoned researchers.

Heat Shock Proteins and Plants provides the most up-to-date and concise reviews and progress on the role of heat shock proteins in plant biology, structure and function and is subdivided into chapters focused on Small Plant HSPs (Part I), Larger Plant HSPs (Part II) and HSPs for Therapeutic Gain (Part III). This book is written by eminent leaders and experts from around the world and is an important reference book and a must-read for undergraduate, postgraduate students and researchers in the fields of Agriculture, Botany, Crop Research, Plant Genetics and Biochemistry, Biotechnology, Drug Development and Pharmaceutical Sciences.

This volume focuses on applications of split inteins, and the progress that has been made in the past 5 years on discovery and engineering of fast and more efficient split inteins. The first few chapters in Split Inteins: Methods and Protocols explore new techniques on how to use split inteins for affinity purification of overproduced proteins, and split-intein based technologies to prepare cyclic peptides and proteins. The next few chapters discuss semisynthetic protein trans-splicing using one synthetic intein piece, synthetic intein-extein pieces used to deliver other cargos for chemical modification both of purified proteins and of proteins in living cells, as well as isotopic labeling of proteins for NMR studies, and a discussion on how protein block copolymers can be generated by protein trans-splicing to form protein hydrogels. The last few chapters deal with intein applications in transgenic plants and conditional inteins that can be regulated in artificial ways by small molecules or light, a cassette-based approach to quickly test many intein insertion positions, and a computational approach to predict new intein split sites (the approach also works for other proteins). Written in the highly successful Methods in Molecular Biology series format, chapters include introduction 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, Split Inteins: Methods and Protocols is a valuable resource that will provide guidance toward possibilities of split intein applications, explore proven and detailed protocols adaptable to various research projects, and inspire new method developments.

Recent work has begun to elucidate at the molecular level how albumin is handled by the kidney and how albuminuria develops in various proteinuric diseases including minimal change disease and focal segmental glomerulosclerosis. This volume provides a comprehensive overview of the renal handling of albumin - from basic mechanisms to the pathophysiology of proteinuric diseases. In describing the basic mechanisms of albuminuria, a particular highlight will be the focus on advanced imaging techniques such as intravital microscopy that have allowed a detailed "window" into albumin transit through the kidney. The volume will cover the epidemiological studies which show that albuminuria is a strong and independent marker of kidney disease progression and cardiovascular events, the molecular details of albumin handling in the kidney at the level of the glomerulus and the proximal tubule and the pathophysiology of proteinuric diseases including minimal change disease, membranous nephropathy, focal segmental glomerulosclerosis and diabetic nephropathy.

Using a novel approach that combines high temporal resolution of the laser T-jump technique with unique sets of fluorescent probes, this study unveils previously unresolved DNA dynamics during search and recognition by an architectural DNA bending protein and two DNA damage recognition proteins. Many cellular processes involve special proteins that bind to specific DNA sites with high affinity. How these proteins recognize their sites while rapidly searching amidst ~3 billion nonspecific sites in genomic DNA remains an outstanding puzzle. Structural studies show that proteins severely deform DNA at specific sites and indicate that DNA deformability is a key factor in site-specific recognition. However, the dynamics of DNA deformations have been difficult to capture, thus obscuring our understanding of recognition mechanisms. The experiments presented in this thesis uncover, for the first time, rapid (~100-500 microseconds) DNA unwinding/bending attributed to nonspecific interrogation, prior to slower (~5-50 milliseconds) DNA kinking/bending/nucleotide-flipping during recognition. These results help illuminate how a searching protein interrogates DNA deformability and eventually "stumbles" upon its target site. Submillisecond interrogation may promote preferential stalling of the rapidly scanning protein at cognate sites, thus enabling site-recognition. Such multi-step search-interrogation-recognition processes through dynamic conformational changes may well be common to the recognition mechanisms for diverse DNA-binding proteins.

This book covers the latest developments in capillary electrophoresis-mass spectrometry for the analysis of therapeutic proteins. The application of capillary electrophoresis-mass spectrometry (CE-MS) coupling technology in the analysis of recombinant therapeutic proteins is detailed thoroughly. Specific topics include recent developments in coupling capillary electrophoresis with mass spectrometry for the quality control of monoclonal antibody therapeutics, top-down analysis of monoclonal antibody using the CE-MS platform, and detection of host cell protein impurities. Comprehensive characterization of antibody-drug conjugates (ADCs) by coupling capillary electrophoresis with mass spectrometry is also covered. This is an ideal book for scientists in the life science and biopharmaceutical industry who are working on characterizing the PTMs of monoclonal antibodies, as well as graduate students and researchers in the separation science and biological mass spectrometry fields.

This volume presents the most recent technologies used in the Polycomb Group Proteins (PcG) field. Chapters detail state-of-the-art methods, creating a unique and comprehensive reference source for investigating Polycomb function in the nucleus. 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, Polycomb Group Proteins: Method and Protocols aims to ensure successful results in the further study of this vital field.

This second edition expands on the previous edition with new chapters that are suitable for newcomers, as well as more detailed chapters that cover protein stability and storage, avoiding proteolysis during chromatography, protein quantitation methods including immuno-qPCR, and the challenges that scale-up of production poses to the investigator. Many of the chapters also discuss generation and purification of recombinant proteins, recombinant antibody production, and the tagging of proteins as a means to enhance their solubility and simplify their purification on an individual scale or in high-throughput systems. This book also provides readers with chapters that describe not just the more commonly used methods, but also recently developed approaches such as proteomic/mass spectrometric techniques and Lectin-based affinity chromatography. 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 Chromatography: Methods and Protocols, Second Edition is a valuable resource for anyone who is interested in the field of protein chromatography.

This volume provides a comprehensive guide on the Cyr61 (Cysteine-rich 61) (CCN) family of proteins and genes from basic research to cutting-edge methodologies and state-of-the-art techniques. Chapters details practical tips to overcome any obstacles with experimentation pertaining to chemistry, biology, physiology, pathology, medical and dental sciences and pharmacology of CCN proteins. 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, CCN Proteins: Methods and Protocols will be a valuable resource for a wide audience, ranging from the experienced CCN researchers looking for new approaches to junior graduate students just beginning in CCN research.

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.

This book highlights key technologies and identifies areas for further development in proteogenomics. The utility and usefulness of very large Omics data sets (Next Gen Sequencing of DNA, RNA-seq, ribosome profiling, mass spectrometry- and antibody-based proteomics) is discussed and opportunities and challenges of related bioinformatics applications are outlined. The reader will be able to appreciate the interdisciplinary nature of the continuously evolving area of proteogenomics, which has already grown beyond its original concept of verifying gene annotations by proteomics. The chapters presented in this book are arranged to offer a general overview, rather than to provide detailed descriptions of technologies. The selected applications will provide useful insight into the level of detail that can be obtained in relation to certain diseases areas, including cancer biology and personalized medicine. The readers will find that each chapter delivers a comprehensive approach to proteogenomics, each from the point of view of a specific application. Research scientists interested in innovative processes that can offer a unique and at the same time a more complete access to technological developments and concepts that in turn can contribute to a better understand biological functions should read this book.

This is the second edition of a very well received book that details how the sumoylation system functions and how it modulates numerous cellular activities. SUMO is a post-translational modifier in the ubiquitin super-family that has gained recognition over the last twenty years as an essential and prevalent regulatory molecule. Individual chapters explore the biochemistry, molecular biology, and cell biology of the sumoylation system and its substrate proteins. The book is divided into three themed parts: Molecular Functions (I), Cell Growth Regulation (II), and Diseases (III). Parts I and II focus on the contribution of sumoylation to cellular activities in both the nuclear and cytoplasmic compartments. The nuclear activities covered include nucleic acid metabolism (both RNA and DNA), chromosome structure and replication, and nucleocytoplasmic transport. Cytoplasmic processes presented include regulation of membrane ion channels, general metabolism, and apoptotic signalling. Topics in Part III include the role of sumoylation in developmental abnormalities (craniofacial and cardiovascular), diabetes, neurodegenerative diseases, cancer, and infections with viruses and bacteria. Each of the corresponding chapter authors is an active researcher who has made significant contributions to understanding sumoylation. This second edition provides updates and revisions to most of the original chapters plus adds six new chapters to address important developing areas of sumoylation research. This volume is intended for a scientific audience from undergraduates to independent researchers. The content will serve as both a solid introduction for the novice reader and an in depth treatment for the advanced scholar.

This detailed collection covers how the biological functions of histone deacetylases (HDACs) and histone acetyltransferases (HATs) can be detected in various experimental settings, both in vivo and in vitro. The book also covers the generation and specificity of deacetylase inhibitors and how such agents can be used to test experimental hypotheses. Written for the popular 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, as well as tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, HDAC/HAT Function Assessment and Inhibitor Development: Methods and Protocols serves as an ideal guide to this vital area of study.

Due to continuous technical developments and new insights into the high complexity of neurological diseases, there is an increasing need for the application of proteomic technologies which can yield potential biomarker readouts for improved clinical management as well as for the development of new drugs by struggling pharmaceutical companies. This book describes the step-by-step use of proteomic methods such as two-dimensional gel electrophoresis, multiplex immunoassay, liquid chromatography mass spectrometry (LC-MS) and selective reaction monitoring MS, to increase our understanding of these diseases, with the ultimate aim of improving patient care. The volume will be of high interest to clinical scientists, physicians and pharmaceutical company scientists as it gives insights into the latest technologies enabling the revolution of personalized medicine. It is of direct interest to both technical and bench biomarker scientists as it gives step by step instructions on how to carry out each of the protocols. It is also of interest to researchers as each technique will be presented in the context of a specific neurological disorder, including Alzheimer's disease, multiple sclerosis, autism spectrum disorders, schizophrenia, major depressive disorder and bipolar disorder. Finally, it will also highlight the future research efforts in this field, which are endeavoring to convert proteomic platforms to the form of hand held devices which can be used in a point of care setting and return diagnostic results within the timeframe of a visit to the general practitioner.

This volume presents relevant background information to understanding the molecular basis governing unconventional protein secretion (UPS), and in particular explores the latest techniques and protocols that have been successfully applied for the study of this topic. Detailed chapters include an overview of conventional and unconventional secretory pathways along with multidisciplinary approaches and methods used for UPS analysis in different organisms. 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, Unconventional Protein Secretion: Methods and Protocols will be useful for all interested in the secretory pathway field as well as applications in cell biology, cell development, biomedical research, and healthcare.

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.

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.

This volume highlights the role of proteostasis in human health and associated disease model systems, reflecting its rising importance which has led to the development of new technologies to obtain insight into underling protein mechanistic events. 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, Proteostasis: Methods and Protocols aims to become a reference book on proteostasis in human health.

This thorough volume explores predicting one-dimensional functional properties, functional sites in particular, from protein sequences, an area which is getting more and more attention. Beginning with secondary structure prediction based on sequence only, the book continues by exploring secondary structure prediction based on evolution information, prediction of solvent accessible surface areas and backbone torsion angles, model building, global structural properties, functional properties, as well as visualizing interior and protruding regions in proteins. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detail and implementation advice to ensure success in the laboratory. Practical and authoritative, Prediction of Protein Secondary Structure serves as a vital guide to numerous state-of-the-art techniques that are useful for computational and experimental biologists.

This volume covers an array of techniques available for studying SH2 domains and phosphotyrosine signaling. The book is divided into six parts: Part I outlines the history of SH2, technology development, and cell signaling; Part II focuses on computational approaches and tools used for identification, classification, and predictions of SH2 domain binding partners; Part III details various ways to prepare the SH2 domains as experimental reagents; Part IV presents methods for structural analysis and conventional binding assays using SH2 domains; Part V describes high-throughput and proteomics approaches to aid in analyzing SH2-mediated interactions; and Part VI covers applications for SH2 domain to functional and imaging analyzes. 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, SH2 Domains: Methods and Protocols is a valuable resource for computational biologists, biochemists, structural biologists, cell biologists, pathologists, and people interested in SH2 domains and phosphotyrosine signaling. Researchers who are investigating how protein interaction domain mediate specificity in signaling systems may also find this book informative.

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.

This volume provides methods for modern macromolecular crystallography, including all steps leading to crystal structure determination and analysis. 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 Crystallography aims to ensure successful results in the further study of this vital field.