Daniel C. Liebler masterfully introduces the science of proteomics by spelling out the basics of how one analyzes proteins and proteomes, and just how these approaches are then employed to investigate their roles in living systems. He explains the key concepts of proteomics, how the analytical instrumentation works, what data mining and other software tools do, and how these tools can be integrated to study proteomes. Also discussed are how protein and peptide separation techniques are applied in proteomics, how mass spectrometry is used to identify proteins, and how data analysis software enables protein identification and the mapping of modifications. In addition, there are proteomic approaches for analyzing differential protein expression, characterizing proteomic diversity, and dissecting protein-protein interactions and networks.

A Unified Microscopic Approach to Analyzing Complex Processes in Molecular Motors Motor Proteins and Molecular Motors explores the mechanisms of cellular functioning associated with several specific enzymatic molecules called motor proteins. Motor proteins, also known as molecular motors, play important roles in living systems by supporting cellular transport and force generation via the transformation of chemical energy into mechanical work. The book presents established results, theoretical methods, and experimental observations related to biological molecular motors. It uses fundamental physical-chemical concepts and methods to develop a systematic theoretical framework for understanding motor protein dynamics. The author introduces the main ideas using simple arguments that avoid heavy mathematical derivations in favor of more intuitive physical understanding. Although the book assumes some rudimentary knowledge of cell biology, calculus, and basic ideas from chemistry and physics, it gives explanations and derivations for most results. Accessible to students and researchers in a wide range of scientific fields, this book provides a unified molecular picture for analyzing motor proteins. It connects major experimental facts on molecular motors to principal theoretical concepts consistent with the fundamental laws of chemistry and physics.

Introduction to Computational Proteomics introduces the field of computational biology through a focused approach that tackles the different steps and problems involved with protein analysis, classification, and meta-organization. The book starts with the analysis of individual entities and works its way through the analysis of more complex entities, from protein families to interactions, cellular pathways, and gene networks. The first part of the book presents methods for identifying the building blocks of the protein space, such as motifs and domains. It also describes algorithms for assessing similarity between proteins based on sequence and structure analysis as well as mathematical models, such as hidden Markov models and support vector machines, that are used to represent protein families and classify new instances. The second part covers methods that investigate higher order structure in the protein space through the application of unsupervised learning algorithms, such as clustering and embedding. The book also explores the broader context of proteins. It discusses methods for analyzing gene expression data, predicting protein-protein interactions, elucidating cellular pathways, and reconstructing gene networks. This book provides a coherent and thorough introduction to proteome analysis. It offers rigorous, formal descriptions, along with detailed algorithmic solutions and models. Each chapter includes problem sets from courses taught by the author at Cornell University and the Technion. Software downloads, data sets, and other material are available at biozon.org

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.

New insights into the evolution and nature of proteins

Exploring several distinct approaches, this book describes the methods for comparing protein sequences and protein structures in order to identify homologous relationships and classify proteins and protein domains into evolutionary families. Readers will discover the common features as well as the key philosophical differences underlying the major protein classification systems, including Pfam, Panther, SCOP, and CATH. Moreover, they'll discover how these systems can be used to understand the evolution of protein families as well as understand and predict the degree to which structural and functional information are shared between relatives in a protein family.

Edited and authored by leading international experts, "Protein Families "offers new insights into protein families that are important to medical research as well as protein families that help us understand biological systems and key biological processes such as cell signaling and the immune response. The book is divided into three sections: Section I: Concepts Underlying Protein Family Classification reviews the major strategies for identifying homologous proteins and classifying them into families.Section II: In-Depth Reviews of Protein Families focuses on some fascinating super protein families for which we have substantial amounts of sequence, structural and functional data, making it possible to trace the emergence of functionally diverse relatives.Section III: Review of Protein Families in Important Biological Systems examines protein families associated with a particular biological theme, such as the cytoskeleton.

All chapters are extensively illustrated, including depictions of evolutionary relationships. References at the end of each chapter guide readers to original research papers and reviews in the field.

Covering protein family classification systems alongside detailed descriptions of select protein families, this book offers biochemists, molecular biologists, protein scientists, structural biologists, and bioinformaticians new insight into the evolution and nature of proteins.

This book is concerned with applications of spectroscopic methods to determine protein structure in solution. The methods which are covered include virtually every method which involves the interaction of electromagnetic radiation with proteins in solution and the chapters are written by acknowledged experts from industry and academic institutions. The reader will be able to use this book to decide which spectroscopic techniques will be applicable to the problem he is faced with and be referred to the primary literature which should be most helpful.

Using a geometric perspective, Protein Geometry, Classification, Topology, and Symmetry reviews and analyzes the structural principals of proteins with the goal of revealing the underlying regularities in their construction. It also reviews computer methods for structure analysis and the automatic comparison and classification of these structures with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of protein classification, the authors explore more abstract geometric and topological representations, including the occurrence of knotted topologies. The book concludes with a consideration of the origin of higher-level symmetries in protein structure. The authors focus on simple geometric methods that are deterministic rather than probabilistic and on the more abstract simplifications of protein structure that allow a better understanding of the overall fold of the structure. Most of the methods described in this book have corresponding computer programs. These can be found (as C source code) at the ftp site of the Division of Mathematical Biology at the National Institute for Medical Research. This collection of ideas contains pedagogical material that make it ideal for post-graduate courses as well as new ideas and results essential for researchers investigating protein structures.

Offers coverage of the development of protein purification processes for large-scale commercial operations, and addresses process development, scale-up, applications and mathematical descriptions. Technologies currently used at the commercial scale are covered in depth.

Lectins have in the past been regarded by many scientists as curious proteins of uncertain structure and specificity that bind to carbohydrates of dubious significance themselves. All this is rapidly changing. The functional importance of glycosylation in cell-cell and cell-pathogen interactions, as well as intracellular events, has been recognized by the explosion of the science of glycobiology. This has been paralleled by the realization that lectins, once they have been well characterized, can be extremely useful tools for exam- ing structural changes in glycosylation and their functional consequences for human pathophysiology. Different lectins vary considerably in their degree of specificity. Some, such as wheatgerm agglutinin, have fairly broad specificity (for glucosamine or sialic acid), whereas others, such as Maackia amurensis, are specific not only for a single carbohydrate, but also for its linkage (2-3 linked sialic acid). Lectins with relatively broad specificity may be very useful as an adjunct to isolation or quantification of soluble glycoproteins, whereas lectins of known, and precise, specificity will be more useful for characterization of carbo- drate structure. We have included an appendix in Lectin Methods and Pro- cols that provides the known specificities of all lectins cited in the text.

"Amino Acid Metabolism, 3rd Edition" covers all aspects of the biochemistry and nutritional biochemistry of the amino acids. Starting with an overview of nitrogen fixation and the incorporation of inorganic nitrogen into amino acids, the book then details other major nitrogenous compounds in micro-organisms, plants and animals. Contents include a discussion of the catabolism of amino acids and other nitrogenous compounds in animals, and the microbiological reactions involved in release of nitrogen gas back into the atmosphere. Mammalian (mainly human) protein and amino acid requirements are considered in detail, and the methods that are used to determine them.

Chapters consider individual amino acids, grouped according to their metabolic origin, and discussing their biosynthesis (in plants and micro-organisms for those that are dietary essentials for human beings), major metabolic roles (mainly in human metabolism) and catabolism (again mainly in human metabolism). There is also discussion of regulatory mechanisms for all these metabolic pathways, and of metabolic and genetic diseases affecting the (human) metabolism of amino acids.

Throughout the book the emphasis is on the nutritional importance of amino acids, integration and control of metabolism and metabolic and other disturbances of relevance to human biochemistry and health. Completely revised edition of this comprehensive text covering all the latest findings in amino acid metabolism researchWritten by an authority in the field Covers new advances in structural biologyClear illustrations of all structures and metabolic pathwaysFull list of recommended further reading for each chapter and bibliography of papers cited in the text

The edition details methods to study intrinsically disordered proteins (IDPs) including recent topics such as extremely high-affinity disordered complexes, kinetics that evade established concepts, liquid-liquid phase separation, and novel disorder-driven allosteric mechanisms. 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, Intrinsically Disordered Proteins: Methods and Protocols aims to help scientists with different backgrounds to further their investigations into these fascinating and dynamic molecules. Chapter 24 is available open access under a CC BY 4.0 license via link.springer.com. Chapters "40 and 42 " are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

With the invitation to edit this volume, I wanted to take the opportunity to assemble reviews on different aspects of circadian clocks and rhythms. Although most c- tributions in this volume focus on mammalian circadian clocks, the historical int- duction and comparative clocks section illustrate the importance of various other organisms in deciphering the mechanisms and principles of circadian biology. Circadian rhythms have been studied for centuries, but only recently, a mole- lar understanding of this process has emerged. This has taken research on circadian clocks from mystic phenomenology to a mechanistic level; chains of molecular events can describe phenomena with remarkable accuracy. Nevertheless, current models of the functioning of circadian clocks are still rudimentary. This is not due to the faultiness of discovered mechanisms, but due to the lack of undiscovered processes involved in contributing to circadian rhythmicity. We know for example, that the general circadian mechanism is not regulated equally in all tissues of m- mals. Hence, a lot still needs to be discovered to get a full understanding of cir- dian rhythms at the systems level. In this respect, technology has advanced at high speed in the last years and provided us with data illustrating the sheer complexity of regulation of physiological processes in organisms. To handle this information, computer aided integration of the results is of utmost importance in order to d- cover novel concepts that ultimately need to be tested experimentally.

Understanding Biology Using Peptides: Proceedings of the 19th American Peptide Symposium highlights many of the recent developments in peptide science, with a particular emphasis on how these advances are being applied to basic problems in biology and medicine. Specific topics covered include novel synthetic strategies, peptides in biological signaling, post-translational modifications of peptides and proteins, peptide quaternary structure in material science and disease, and peptides as tools in drug discovery.

About the Editor:

Dr. Sylvie Blondelle is an Associate Member in Microbiology/Biochemistry at Mixture Science, Inc., San Diego, CA and Head of the Biosafety Department at the Burnham Institute for Medical Research. Her research focuses on strategies toward the development an HIV vaccine through optimization of peptide immunogens. Dr. Blondelle received her Ph.D. in organic chemistry from the University of Montpellier, France, in 1988.

Driven by the widespread growth of proteomic practices, protein separation techniques have been refined to minimize variability, optimize particular applications, and adapt to user preferences in the analysis of proteins. Separation Methods in Proteomics provides a comprehensive examination of all major separation techniques for proteomics research. Written as a compilation of hands-on methods exemplified by the work of several recognized leaders in the field, this book may serve as a guide for selection of the optimal separation strategies to solve particular biological problems. Recent progress in the development of robust analytical techniques and instrumentation has created the need for good quality biological samples that are subject to analysis. Emphasizing the importance of sample preparation, the book explains how proteomes can be divided into smaller, less complicated "subproteomes" for individual analysis. It also highlights several hybrid approaches that take into account protein interactions. Including applications of the separation methods currently employed in proteomic analyses for both clinical and basic research, Separation Methods in Proteomics contains practical information that can enhance the current and future endeavors of scientists in proteomics, genomics, transcriptomics, biomarker discovery, and drug discovery.

Although less common than -amino acids, non- -amino acids-where the amino group is not on the carbon immediately adjacent to the carboxyl group but is attached to another carbon in the chain (for example, the , , carbon)-are components of biologically important molecules, are significant in the pharmaceutical industry, and are useful starting materials for many areas of organic chemistry. Since the publication of the first edition of this book nearly 20 years ago, synthetic work devoted to the preparation of non- -amino acids has expanded greatly. Methods of Non- -Amino Acid Synthesis, Second Edition has been extensively rewritten and reorganized, providing an up-to-date review of strategies and methods for non- -amino acid synthesis, particularly those amino acids that are key synthetic intermediates or important compounds in their own right. It focuses on acyclic amino acids of C3-C10, but also aminoalkanoic carboxylic acids, aminoalkenoic acids, and aminoalkynoic acids. The new edition contains many updated references and has a greater emphasis on the biological importance of non- -amino acids. In addition to an array of synthetic methods, the book offers discussions on why non- -amino acids are important. The book covers synthetic methods that rely on substituent refunctionalization, the conversion of cyclic precursors to acyclic amino acids, conjugate addition reactions, and enolate anion reactions and condensation reactions that lead to non- -amino acids. It also examines reactions and strategies that lead to good diastereoselectivity and enantioselectivity during synthesis. A chapter devoted to biologically important amino acids includes separate sections on GABA, GABOB, carnitine, DAVA, statine, and other significant amino acids as well as a new section on peptides and proteins that contain non- -amino acids. The final chapter addresses aminocyclic and heterocyclic amino acids.

This book describes hydration structures of proteins by combining experimental results with theoretical considerations. It is designed to introduce graduate students and researchers to microscopic views of the interactions between water and biological macromolecules and to provide them with an overview of the field. Topics on protein hydration from the past 25 years are examined, most of which involve crystallography, fluorescence measurements, and molecular dynamics simulations. In X-ray crystallography and molecular dynamics simulations, recent advances have accelerated the study of hydration structures over the entire surface of proteins. Experimentally, crystal structure analysis at cryogenic temperatures is advantageous in terms of visualizing the positions of hydration water molecules on the surfaces of proteins in their frozen-hydrated crystals. A set of massive data regarding hydration sites on protein surfaces provides an appropriate basis, enabling us to identify statistically significant trends in geometrical characteristics. Trajectories obtained from molecular dynamics simulations illustrate the motion of water molecules in the vicinity of protein surfaces at sufficiently high spatial and temporal resolution to study the influences of hydration on protein motion. Together with the results and implications of these studies, the physical principles of the measurement and simulation of protein hydration are briefly summarized at an undergraduate level. Further, the author presents recent results from statistical approaches to characterizing hydrogen-bond geometry in local hydration structures of proteins. The book equips readers to better understand the structures and modes of interaction at the interface between water and proteins. Referred to as "hydration structures", they are the subject of much discussion, as they may help to answer the question of why water is indispensable for life at the molecular and atomic level.

Starting from a comprehensive quantum mechanical description, this book introduces the optical (IR, Raman, UV/Vis, CD, fluorescence and laser spectroscopy) and magnetic resonance (1D and 2D-NMR, ESR) techniques. The book offers a timely review of the increasing interest in using spin-label ESR as an alternative structural technique for NMR or X-ray diffraction. Future aspects are treated as well, but only as an illustration of the progress of ESR in this field.

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.

There are 28 different collagens, with 46 unique chains, which allows for a collagen for each time and place. Some collagens are specialized for basement membrane, whereas others are the central structural component of the interstitial matrix. There are eight collagens among the 20 most abundant proteins in the body, which makes these molecules essential building blocks of tissues. In addition, lessons learned from monogenomic mutations in these proteins result in grave pathologies, exemplifying their importance in development. These molecules, and their post-translationally modified products serve as biomarkers of diseases in a range of pathologies associated with the extracellular matrix. Biochemistry of Collagens, Laminins, and Elastin: Structure, Function, and Biomarkers, Second Edition provides researchers and students current data on key structural proteins (collagens, laminins, and elastin), reviews on how these molecules affect pathologies, and information on how selected modifications of proteins can result in altered signaling properties of the original extracellular matrix component. Further, it discusses the novel concept that an increasing number of components of the extracellular matrix harbor cryptic signaling functions that may be viewed as endocrine function, and it highlights how this knowledge can be exploited to modulate fibrotic disease.

Protein Modificomics: From Modifications to Clinical Perspectives comprehensively deals with all of the most recent aspects of post-translational modification (PTM) of proteins, including discussions on diseases involving PTMs, such as Alzheimer's, Huntington's, X-linked spinal muscular atrophy-2, aneurysmal bone cyst, angelman syndrome and OFC10. The book also discusses the role PTMs play in plant physiology and the production of medicinally important primary and secondary metabolites. The understanding of PTMs in plants helps us enhance the production of these metabolites without greatly altering the genome, providing robust eukaryotic systems for the production and isolation of desired products without considerable downstream and isolation processes.

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 volume provides comprehensive protocols on experimental and computational methods that are used to study probe protein folding reactions and mechanisms. Chapters divided into five parts detail protein engineering, protein chemistry, experimental approaches to investigate the thermodynamics and kinetics of protein folding transitions, probe protein folding at the single molecule, analysis and interpretation of computer simulations, procedures and tools for the prediction of protein folding properties. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Protein Folding: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.

This book explores the remarkable information correspondences and probability structures of proteins. Correspondences are pervasive in biochemistry and bioinformatics: proteins share homologies, folding patterns, and mechanisms. Probability structures are just as paramount: folded state graphics reflect Angstrom-scale maps of electron density. The author explores protein sequences (primary structures), both individually and in sets (systems) with the help of probability and information tools. This perspective will enhance the reader's knowledge of how an important class of molecules is designed and put to task in natural systems, and how we can approach class members in hands-on ways.

The American Peptide Society (APS) provides a forum for advancing and promoting knowledge of the chemistry and biology of peptides. The approximately one thousand members of the Society come from North America and from more than thirty other countries throughout the world. Establishment of the APS was a result of the rapid worldwide growth that has occurred in peptide-related research, and of the increasing interaction of peptide scientists with virtually all fields of science. Peptides for Youth: The Proceedings of the the 20th American Peptide Symposium will highlight many of the recent developments in peptide science, with a particular emphasis on how these advances are being applied to basic problems in biology and medicine. The 20th American Peptide Symposium will take place June 26 - 30, 2007 in Montreal, Canada.

This volume details protocols that cover the broad arsenal of techniques used to study a secretion system from A to Z. Chapters focus on identifying and localizing the different subunits, defining interactions within subunits, monitoring conformational changes, purifying and imaging of large complexes, defining the assembly pathway by fluorescence microscopy and the role of energy during assembly and/or secretion, identifying secreted effectors as well as reporters to follow effector transport. 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, Bacterial Protein Secretion Systems: Methods and Protocol aims to provide techniques that are not restricted to the study of secretion systems but are also of specific interest for any researcher interested on multi-protein complexes of the bacterial cell envelope.