The book focuses on the aqueous interface of biomolecules, a vital yet overlooked area of biophysical research. Most biological phenomena cannot be fully understood at the molecular level without considering interfacial behavior. The author presents conceptual advances in molecular biophysics that herald the advent of a new discipline, epistructural biology, centered on the interactions of water and bio molecular structures across the interface. The author introduces powerful theoretical and computational resources in order to address fundamental topics such as protein folding, the physico-chemical basis of enzyme catalysis and protein associations. On the basis of this information, a multi-disciplinary approach is used to engineer therapeutic drugs and to allow substantive advances in targeted molecular medicine. This book will be of interest to scientists, students and practitioners in the fields of chemistry, biophysics and biomedical engineering.

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.

The aim of the book is to discuss the application of molecular pathology in cancer research, and its contribution in the classification of different tumors and identification of potential molecular targets, as well as how this knowledge may be translated into clinical practice, and the huge impact this field is likely to have in the next 5 to 10 years.

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.

This new edited volume in the Springer Subcellular Biochemistry Series presents a comprehensive, state-of-the-art overview of the proteomics of peroxisomes derived from mammalian, Drosophila, fungal, and plant origin, and contains contributions from leading experts in the field. The development of sensitive proteomics and mass spectrometry technologies, combined with bioinformatics approaches now allow the identification of low-abundance and transient peroxisomal proteins and permits to identify the complete proteome of peroxisomes, with the consequent increase of our knowledge of the metabolic and regulatory networks of these important cellular organelles. The book lines-up with these developments and is organized in four sections including: (i) mass spectrometry-based organelle proteomics; (ii) prediction of peroxisomal proteomes; (iii) analysis of peroxisome proteome interaction networks; and (iv) peroxisomes in relation to other subcellular compartments. The editor Luis A. del Rio is Professor ad honorem of the Spanish National Research Council (CSIC) in the Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry and Cell & Molecular Biology of Plants, at the Estacion Experimental del Zaidin, Granada, Spain. Del Rio's research group focuses on the metabolism of reactive oxygen species (ROS), reactive nitrogen species (RNS) and antioxidants in plant peroxisomes, and the ROS- and RNS-dependent role of peroxisomes in plant cell signalling. The editor Michael Schrader is Professor of Cell Biology & Cytopathology in the Department of Biosciences at the University of Exeter, UK. Using mammalian peroxisomes as model organelles, Prof. Schrader and his team aim to unravel the molecular machinery and signalling pathways that mediate and regulate the formation, dynamics and abundance of these medically relevant cellular compartments.

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.

"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 presents the latest developments of the main pillars of protein analysis, such as sample preparation, separation and characterization. The book begins by describing basic but important sample preparation protocols. It then goes on to describe more sophisticated procedures on enriching specific protein classes and concludes with detailed descriptions of integrated work-flows for comprehensive protein analysis and characterization. The authors of the individual chapters are renowned protein biochemists who have all set value to provide a detailed representation of their lab work. Throughout the chapters, these authors share important tips and tricks for a successful and reproducible employment of their protocols in other laboratories. 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, Proteomic Profiling: Methods and Protocols is the perfect guide for students of Biochemistry, Biomedicine, Biology, and Genomics and will be an invaluable source for the experienced, practicing scientists.

Modification of target protein properties by reversible phosphorylation events has been found to be one of the most prominent cellular control processes in all organisms. Recent advances in the areas of molecular biology and biochemistry are presenting new possibilities for reaching an unprecedented depth and a proteome-wide understanding of phosphorylation processes in plants as well as in other species. The major goal of "Plant Kinases: Methods and Protocols" is to provide the experimentalist with a detailed account of the practical steps necessary for successfully carrying out each protocol in his or her own laboratory. Plant protein kinases specifically addressed in this volume are members of the plant MAP kinase cascade, cyclin- and Calcium-dependent protein kinases, and plant sensor and receptor kinases. Written in the highly successful "Methods in Molecular Biology " 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, "Plant Kinases: Methods and Protocols "will prove a useful laboratory companion to both novice and seasoned researchers by facilitating the practical work that will lead them to new and exciting insights in this dynamic field.

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Over the past thirty years, many elegant genetic and biochemical approaches have been combined in order to advance the study of protein secretion and the necessary navigation through cell membranes, yet, despite this progress, less than two hundred membrane protein structures are known, nowhere near the complete inventory that the discovered protein export systems suggest. In Protein Secretion: Methods and Protocols, leading experts in the field provide robust, well-established protocols to elucidate the multiplicity of tools that have been developed to study protein sorting, membrane targeting, transmembrane crossing, and secretion across multiple membranes. With examples involving both prokaryotic and eukaryotic organisms, the volume covers subjects ranging from bioinformatics and proteomics to fundamental enzymology and genetics to cell biology, structural analyses, and biophysics. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the key materials and reagents, step-by-step, readily reproducible protocols, and detailed notes on troubleshooting and avoiding known pitfalls. Comprehensive and dependable, Protein Secretion: Methods and Protocols focuses on well-characterized paradigms so that scientists studying a vast array of subjects from biochemistry and genetics to biotechnology and biopharmaceuticals can benefit and expand upon their vital research.

The development of proteomic analyses using advanced mass spectrometry techniques has revolutionized the way proteins are studied, namely, as individual molecules within a complex system. HIV-1 Proteomics: From Discovery to Clinical Application comprehensively covers protein analysis from the early classic experimental days to current state-of-the-art HIV-1 proteomics in a clear informative style that brings expert-level understanding to the novice. Discussion of important clinical applications and future directions for the field also make this an ideal read for the expert. After finishing this book, the reader will have a complete and functional understanding of protein analysis from traditional biochemistry to modern proteomics.

In Flavins and Flavoproteins: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study flavins and flavoproteins. These include review style methods and protocols to exemplify the variety, the power and the success of modern techniques and methods in application to flavoproteins. Part I of this Volume covers general properties, syntheses and applications of free flavins as well as its analogs and flavoproteins. Part II covers characterizations of flavins and flavoproteins using modern experimental techniques as well as theoretical methods. 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. Thorough and intuitive, Flavins and Flavoproteins: Methods and Protocols aids scientists in continuing to tackle the countless questions that need to be answered to more fully comprehend the vast diversity and specificity of flavin-governed biological processes.

This detailed volume addresses recent developments in phosphoproteomic techniques with a particular focus on the plant system. Over the recent decades, proteomic methods were refined to study the significance and dynamics of protein phosphorylation in various biological contexts. However, working with plant tissue imposes particular challenges to the biologist which are attributed to the rigid cell wall making protein extraction more difficult, the skewed protein abundance with Rubisco as a highly abundant protein and a large central vacuole leading to low protein yield and increased degradative enzyme activity. The methodologies in this book seek to move beyond these issues. Written for the 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. Practical and authoritative, Plant Phosphoproteomics: Methods and Protocols serves as an ideal reference for researchers investigating this vital area of plant science.

The liver is responsible for a wide range of critical functions essential to life, and is composed of several different cell types. In Liver Proteomics: Methods and Protocols, expert researchers in the field detail many of the methods that are used to study the live. These methods include the most up-to-date strategies being used to characterize the liver proteome at the global, cellular, subcellular, post translational and functional level.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, Liver Proteomics: Methods and Protocols seeks to aid scientists in the further study of this crucially important organ.

This volume documents this unique family of cell surface proteins. Despite masquerading as intractable and difficult to clone and characterize, ENOX proteins have and continue to offer remarkable opportunities for research, commercial development and outside confirmation of therapeutic, diagnostic and new paradigms to help explain complex biological processes.

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 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.

The subject of this volume is a comprehensive examination of the biochemistry and biology of all classes of known PAS proteins, with the intention that readers will find insight into their own work and ideas from study of the multitude of PAS protein functions. PAS proteins control numerous physiological and developmental events, and span phylogeny from bacteria to man. Bacterial and plant PAS proteins act as sensors of environmental stimuli, including light, oxygen, and energy status.

Not surprising, given these roles, there is intense investigation of the roles of bHLH-PAS proteins in issues of human health including: (1) cancer induction, (2) cancer growth and vascularity, (3) birth defects, including Down syndrome, (4) appetite control and obesity, (5) sleep rhythm disorders, and (6) mental health disorders such as social interactions and learning.

PAS proteins encompass many fields of biology, and scientists who work in these fields (circadian rhythms, oxygen regulation, toxin metabolism, bacterial sensors, and development) are an audience, particularly those who actively work on PAS proteins and researchers interested in transcriptional control, signal transduction, and evolution.

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 thorough book covers the most recent proteomics techniques, databases, bioinformatics tools, and computational approaches that are used for the identification and functional annotation of proteins and their structure. The most recent proteomic resources widely used in the biomedical scientific community for storage and dissemination of data are discussed. In addition, specific MS/MS spectrum similarity scoring functions and their application in the field of proteomics, statistical evaluation of labeled comparative proteomics using permutation testing, and methods of phylogenetic analysis using MS data are also described in detail. Written for the highly successful Methods in Molecular Biology series, chapters contain the kind of detail and key implementation advice to ensure successful results. Authoritative and cutting-edge, Proteome Bioinformatics serves as a useful resource for researchers who are beginners as well as advanced investigators in the field of proteomics.

Regulated turnover of extracellular matrix (ECM) is an important component of tissue homeostasis. In recent years, the enzymes that participate in, and control ECM turnover have been the focus of research that touches on development, tissue remodeling, inflammation and disease. This volume in the Biology of Extracellular Matrix series provides a review of the known classes of proteases that degrade ECM both outside and inside the cell. The specific EMC proteases that are discussed include cathepsins, bacterial collagenases, matrix metalloproteinases, meprins, serine proteases, and elastases. The volume also discusses the domains responsible for specific biochemical characteristics of the proteases and the physical interactions that occur when the protease interacts with substrate. The topics covered in this volume provide an important context for understanding the role that matrix-degrading proteases play in normal tissue remodeling and in diseases such as cancer and lung disease. The series Biology of Extracellular Matrix is published in collaboration with the American Society for Matrix Biology.

Since the first edition of Protein Nanotechnology Protocols Instruments and Applications the intersection of protein science and nanotechnology has become an exciting frontier in interdisciplinary sciences. The second edition of Protein Nanotechnology Protocols Instruments and Applications expands upon the previous editions with current, detailed chapters that provide examples of proteins which are now being harnessed for a wide range of applications, some more developed than others. This book also delves into engineering proteins and an overview of the sorts of tools that are now readily available to manipulate the structure and function of proteins, both rationally and using methods inspired by evolution. 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, Protein Nanotechnology Protocols Instruments and Applications, Second Edition seeks to provide an overview of this multi-faceted field and a useful guide to those who wish to contribute to it.

This thesis offers readers a comprehensive introduction to amyloid proteins and the computational methods used with them. Katrine Skeby critically assesses and compares both the literature and the experiments performed by other researchers, which further elevates the quality and relevance of her own work. Amyloid proteins are highly complex, and this research provides unparalleled insights, especially with regard to the origin of cytotoxicity and to developing technologies for early detection, revealing in detail the molecular mechanisms behind hIAPP behavior. Several studies within the thesis answer difficult questions which promote future research into the properties of amyloid proteins.

Blurb for Volume 2
Hans Vogel and a panel of leading researchers review the protein chemistry and behavior of this significant class proteins, and provide a comprehensive collection of proven experimental techniques for studying it both in vitro and in vivo. This second volume focuses on cutting-edge experimental techniques for studying the solution structure, stability, dynamics, calcium-binding properties, and biological activity of calcium-binding protein in general. In addition to enzymatic assays and more routine spectroscopic and protein chemistry techniques, there are also NMR approaches, thermodynamic analyses, kinetic measurements such as surface plasmon resonance, strategies for amino acid sequence alignments, and fluorescence methods to study the distribution of calcium and calcium-binding proteins in cells. The first companion volume, Reviews and Case Histories sets the stage for this volume by introducing the various classes of intra- and extra-cellular calcium-binding proteins and their mode of action.
Single Blurb for Both Volumes
Hans Vogel and a panel of leading researchers review the protein chemistry and behavior of this significant protein class, and provide a comprehensive collection of proven experimental techniques for their study both in vitro and in vivo. The first volume discusses the role of calcium in intracellular secondary messenger activation mechanisms, including unique aspects of calcium chemistry and its utilization in dairy proteins and blood clotting. Detailed case studies provide a wealth of valuable information about protein purification and characterization strategies, X-ray crystallography, and specific calcium-binding proteins andtheir modes of action. The second volume focuses on cutting-edge experimental techniques for studying the solution structure, stability, dynamics, calcium-binding properties, and biological activity of calcium-binding protein in general. In addition to enzymatic assays and more routine spectroscopic and protein chemistry techniques, there are also NMR approaches, thermodynamic analyses, kinetic measurements such as surface plasmon resonance, strategies for amino acid sequence alignments, and fluorescence methods to study the distribution of calcium and calcium-binding proteins in cells.