Glycosylation is the most abundant post-translational modification of proteins. Estimates vary widely, but a common assessment is that upwards of 50% of eukaryotic proteins are modified by some type of glycan. In Mass Spectrometry of Glycoproteins: Methods and Protocols, expert researchers in the field detail many of the methods that are now commonly used for glycoproteomics. These methods and techniques include robust sample preparation techniques; advanced chromatographic strategies for improving dynamic range; state-of-the-art mass spectrometry instrumentation and associated ionization and fragmentation methods; and informatics tools used for identifying glycoproteins and characterizing the associated glycans. 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, Mass Spectrometry of Glycoproteins: Methods and Protocol is an essential resource for those who work at the interface of glycobiology and mass spectrometry.

Protein analysis is increasingly becoming a cornerstone in deciphering the molecular mechanisms of life. Proteomics, the large-scale and high-sensitivity analysis of proteins, is already pivotal to the new life sciences such as Systems Biology and Systems Medicine. Proteomics, however, relies heavily on the past and future advances of protein purification and analysis methods. DIGE, being able to quantify proteins in their intact form, is one of a few methods that can facilitate this type of analysis and still provide the protein isoforms in an MS-compatible state for further identification and characterization with high analytical sensitivity. Differential Gel Electrophoresis: Methods and Protocols introduces the concept of DIGE and its advantages in quantitative protein analysis. It provides detailed protocols and important notes on the practical aspects of DIGE with both generic and specific applications in the various areas of Quantitative Proteomics. Divided into four concise sections, this detailed volume opens with the basics of DIGE, the technique and its practical details with a focus on the planning of a DIGE experiment and its data analysis. The next section introduces various DIGE methods from those employed by scientists world-wide to more novel methods, providing a glance at what is on the horizon in the DIGE world. The volume closes with an overview of the wide range of DIGE applications from Clinical Proteomics to Animal, Plant, and Microbial Proteomics applications. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Differential Gel Electrophoresis: Methods and Protocols can be used by novices with some background in biochemistry or molecular biology as well as by experts in Proteomics who would like to deepen their understanding of DIGE and its employment in many hyphenations and application areas. With its many protocols, applications, and methodological variants, it is also a unique reference for all who seek fundamental details on the working principle of DIGE and ideas for possible future uses of DIGE in novel analytical approaches.

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.

Poly (ADP-ribose) Polymerases (PARPs) are abundant and ubiquitous proteins that regulate crucial processes of the cell cycle, DNA repair, genomic stability, and transcriptional regulation. Being involved in basic cell functions, PARPs mediate rapid responses to such environmental factors as stress, infection, nutrition and hormonal signals. Whereas PARP inhibitors can suppress tumor growth and proliferation in certain breast, ovarian, and prostate cancers, understanding how PARP controls cellular functions is essential for the development of novel cancer treatments strategies. Divided into three convenient sections, Poly(ADP-Ribose) Polymerase: Methods and Protocols aims to explain how PARP proteins act within the normal development of an organism as well as in pathogenic conditions, seeks to advance the knowledge of developmental pathways regulation, and endeavors to facilitate the development of new therapeutic drugs and methods to target PARP-dependent processes. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Poly(ADP-Ribose) Polymerase: Methods and Protocols serves as an ideal guide to scientists who wish to continue exploring this exciting and progressive research field.

Membrane proteins play key roles in numerous cellular processes, in particular mediating cell-to-cell communication and signaling events that lead to a multitude of biological effects. Membrane proteins have also been implicated in many critical diseases such as atherosclerosis, hypertension, diabetes and cancer. In Membrane Protein Structure Predictions Methods: Methods and Protocols, expert researcher in the field detail the advances in both experimental and computational approaches of the structure, dynamics and interactions of membrane proteins dividing the volume into two sections. The first section details the procedures used for measurements of structure and dynamics of membrane proteins. While the second section contains a survey of the computational methods that have played a critical role in membrane protein structure prediction as well as in providing atomic level insight into the mechanism of the dynamics of membrane receptors. Written in the highly successful Methods in Molecular Biology (TM) 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, Membrane Protein Structure Predicitons: Methods and Protocols seeks to aid scientists in the further study of membrane protein structure and function.

Proteins are the functional units of the cellular machinery and they provide significant information regarding the molecular basis of health and disease. Therefore, techniques to separate and isolate the various proteins are critical to studying and understanding their functional characteristics. One of the widely used techniques for this purpose is electrophoresis. In Protein Electrophoresis: Methods and Protocols, contributions from experts in the field have been collected in order to provide practical guidelines to this complex study. Each chapter outlines a specific electrophoretic variant in detail so that laboratory scientists may perform a technique new to their lab without difficulty. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Protein Electrophoresis: Methods and Protocols seeks to serve laboratory scientists with well-honed, detailed methodologies in an effort to further our knowledge of this essential field.

The genomes of cellular organisms are organized as double-stranded DNA, a structure that must be unwound to provide DNA replication, recombination, and repair machinery access to genomic information. However, DNA unwinding comes with inherent risks to genome stability. To help mediate these risks, bacterial, archael, and eukaryotic cells have evolved protective ssDNA-binding proteins (SSBs) that bind ssDNA with high affinity and specificity. SSBs also aid genome metabolic processes through direct interactions with key proteins in genome maintenance enzymes. Single-Stranded DNA Binding Proteins: Methods and Protocols assembles methods developed for examining the fundamental properties of SSBs and for exploiting the biochemical functions of SSBs for their use as in vitro and in vivo reagents. Clearly and concisely organized, the volume opens with an introduction to the structures and functions of SSBs, followed protocols for studying SSB/DNA complexes, methods for studying SSB/heterologous protein complexes, protocols for interrogating post-translational modifications of SSBs, and concludes with uses of fluorescently-labeled SSBs for in vitro and in vivo studies of genome maintenance processes. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Single-Stranded DNA Binding Proteins: Methods and Protocols provides a rich introduction for investigators who are interested in this fascinating family of DNA-binding proteins.

Cytochromes P450 (CYPs) comprise a large superfamily of proteins that are of central importance in the detoxification or activation of a tremendous number of natural and synthetic hydrophobic xenobiotics, including many therapeutic drugs, chemical carcinogens and environmental pollutants. CYPs are important in mediating interactions between an organism and its chemical environment and in the regulation of physiological processes. Cytochrome P450 Protocols, Third Edition focuses on high-throughput methods for the simultaneous analysis of multiple CYPs, substrates or ligands. Although the emphasis is on CYPs of mammalian origin, it reflects an increasing interest in CYPs of bacterial species. Also included are chapters on cytochrome P450 reductase (the redox partner of CYPs) and the flavin-containing monooxygenases (FMOs), and metabolomic and lipidomic approaches for identification of endogenous substrates of CYPs ('de-orphanizing' CYP substrates). Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Cytochrome P450 Protocols, Third Edition provides a wide range of techniques accessible to researchers in fields as diverse as biochemistry, molecular biology, pharmacology, toxicology, environmental biology and genetics.

This unique text introduces students and researchers to the world of misfolded proteins, toxic oligomers, and amyloid assemblages, and the diseases of the brain that result. During the past few years the connections between failures in protein quality control and neurological disorders have been reinforced and strengthened by discoveries on multiple fronts. These findings provide novel insights on how amyloidogenic oligomers and fibrils form, interconvert from one state to another, and propagate from cell to cell and region to region. Starting with protein folding and protein quality control basics, the reader will learn how misfolded proteins can cause diseases ranging from prion diseases to Alzheimer's disease and Parkinson's disease to Huntington's disease, amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Authoritative but written in a clear and engaging style, Fundamentals of Neurodegeneration and Protein Misfolding Disorders addresses one of today's forefront areas of science and medicine. The text emphasizes the new groundbreaking biophysical and biochemical methods that enable molecular-level explorations and the conceptual breakthroughs that result. It contains separate chapters on each of the major disease classes. Special emphasis is placed on those factors and themes that are common to the diseases, especially failures in synaptic transmission, mitochondrial control, and axonal transport; breakdowns in RNA processing; the potential role of environmental factors; and the confounding effects of neuroinflammation. The book is ideal for use in teaching at the advanced undergraduate and graduate levels, and serves as a comprehensive reference for a broad audience of students and researchers in neuroscience, molecular biology, biological physics and biomedical engineering.

This book covers the state-of-the-art of modern MALDI (matrix-assisted laser desorption/ionization) and its applications. New applications and improvements in the MALDI field such as biotyping, clinical diagnosis, forensic imaging, and ESI-like ion production are covered in detail. Additional topics include MS imaging, biotyping/speciation and large-scale, high-speed MS sample profiling, new methods based on MALDI or MALDI-like sample preparations, and the advantages of ESI to MALDI MS analysis. This is an ideal book for graduate students and researchers in the field of bioanalytical sciences. This book also: * Showcases new techniques and applications in MALDI MS * Demonstrates how MALDI is preferable to ESI (electrospray ionization) * Illustrates the pros and cons associated with biomarker discovery studies in clinical proteomics and the various application areas, such as cancer proteomics

Tryptophan metabolism via kynurenine pathway plays a critical role in both health and a variety of human diseases. This book highlights the known associations between kynurenine pathway and various disease states, as well as examines the current status of drug development and clinical trials of compounds known to alter tryptophan metabolism. The research plays a critical role in molecular targeted therapies directed at altering the kynurenine pathway of tryptophan metabolism. The initial and rate-limiting step of tryptophan metabolism is mediated by one of two enzymes, tryptophan-2,3-dioxygenase (TDO; predominantly in the liver, but also in the brain) and indoleamine-2,3-dioxygenase (IDO; in a host of tissues in response to immune activation). Targeting the enzymes IDO and TDO, as well as other downstream effectors would therefore be likely to generate novel treatment options that would be helpful in a wide variety of clinical settings. This book provides a unique bridge between basic mechanistic understanding of the role of the kynurenine pathway with translational applications and clinical relevance. It will explore the indications that tryptophan metabolism is a potential biomarker of disease activity, can contribute to local and possibly systemic immune suppression in cancer, and is an attractive target for which a variety of inhibitors are readily available.

This book is dedicated to the channels and pores that belong to an eclectic and ubiquitous class of unconventional - perhaps at times strange - pore-forming molecules, which nevertheless play fundamental roles in various organisms. These non-canonical channels may take on various and sometimes complex architectures, such as large beta-barrels or lipid-containing pores. They may originate from bacteria, viruses or intracellular organelles. For some of them, the physiologically relevant substrate may indeed be ions, and for others folded polypeptides. Some are released by cells in a soluble form that has the ability to insert into biological membranes to exert its permeabilizing effect. Many of these unconventional pores have been investigated by electrophysiology, which, by its virtue of focusing on a few or even a single unit, has provided invaluable insight into the mechanisms and structure-function relationships of these remarkable membrane entities. The chapters of this book highlight a representative set of these interesting investigations.

This second of two volumes discusses subfamily proteins which function in molecular and vesicular transport mechanisms inside the cell. In this volume the focus lies on the Rab, Ran and Arf subfamily members. As in Volume 1, the book is written by international renowned scientists in the field of small G-proteins. In elaborate reviews, biochemistry, structure, function and G-protein - effector interactions are described. Together with Volume 1 this book provides an comprehensive state-of-the-art work on small G-proteins (GTPases). It is written for Graduates and Professors in Biochemistry and Cell Biology interested in the mechanism and function of small G-proteins but are extremely valuable for those who want to move into the field.

This excellent book covers wide-ranging topics in interdisciplinary microbiology, addressing various research aspects and highlighting advanced discoveries and innovations. It presents the fascinating topic of modern biotechnology, including agricultural microbiology, microalgae biotechnology, bio-energy, bioinformatics and metagenomics, environmental microbiology, enzyme technology and marine biology. It presents the most up-to-date areas of microbiology with an emphasis on shedding light on biotechnological advancements and integrating these interdisciplinary microbiology research topics into other biotechnology sub-disciplines. The book raises awareness of the industrial relevance of microbiology, which is key component of this unique collection. The topics include production of antioxidant-glutathione, enzyme-engineering methods, probiotic microbiology and features of microbial xylanases. It also covers some other remarkable aspects of microbiology, like potential health hazards in recreational water and fullerene nanocomposites, which are vital for biotechnological interventions. This book will be valuable resource for senior undergraduate and graduate students, researchers and other interested professionals or groups working in the interdisciplinary areas of microbiology and biotechnology.

'Antibacterial Surfaces' covers the advances being made in the design of antibacterial surfaces, which have the ability to either prevent the initial attachment of bacterial cells, or kill any cells that come into contact with these surfaces. This book discusses the mechanisms associated with the attachment of bacteria to surfaces and the main strategies currently being employed to control the initial attachment processes. These strategies are expanded upon in the subsequent chapters, where the definition and description of antibacterial surfaces are clarified, as are the mechanisms that come into play when determining the effectiveness of an antibacterial surface. Subsequent chapters discuss a number of naturally occurring antibacterial surfaces, the methods currently being used for producing synthetic antibacterial surfaces, and the current and potential applications of such materials. This book will be of great interest to people who work with materials that need to remain free of bacterial films, from designing safer biomedical implants to the production of self-cleaning materials where the prevention of biofilm formation has significant economic advantages.

This book is intended for scientifc researchers, clinical laboratorians, clinical and translational scientists, and others interested in proteomics and biomarker discovery. Urine is one of the most easily accessible biological samples, and it provides a treasure trove of molecules important in clinical diagnostics. In this book, we review briefly the classical urine tests that are performed in the clinical laboratory and then delve into the state-of-the-art methods for proteomic analysis using urine specimens. The most recent advances are discussed with regard to sample preparation, data analysis, and fnally methods and applications. A multitude of examples are provided including procedural details for the identifcation and characterization of urine biomarkers that hold potential for the diagnosis and treatment of many different disease conditions. The text is arranged so as to read systematically: introduction, sample preparation methods, applications, and data analysis. However, it does not necessarily require the reader to read it from start to fnish. Each chapter is organized such that it can be read individually without requiring knowledge from other chapters. I would like to thank the many individuals who made this book possible. These include the many authors who contributed to each of the individual chapters, the corresponding authors who took responsibility in providing the complete and fnished versions solicited for the peer review process, and the many scientifc reviewers who provided their valuable input and guidance.

Amyloid diseases are characterized by the deposition of insoluble fibrous amyloid proteins. The word "amyloid" indicates a starch-like compound, and though a misnomer, continues to be the accepted term for this group of protein conformational disorders. The second edition of Amyloid Proteins expands upon the previous edition with current, detailed protocols for the preparation of amyloid and its precursors, specific analytical methods for studying these proteins, cell culture models and assays for production of amyloid proteins, and protocols for amyloid extraction from tissue, its detection in vitro and in vivo, as well as nontransgenic methods for developing amyloid mouse models. 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, Amyloid Proteins, Second Edition seeks to aid scientists in the amyloid field to establish new techniques in their laboratories. Authoritative and practical, Amyloid Proteins, Second Edition seeks to aid scientists in the amyloid field to establish new techniques in their laboratories.

Through all of the recent progress provided by high throughput DNA sequencing technologies, it has become clearer and clearer that the study of proteins and protein organelles will be the key to unlocking our ability to manipulate cells and intervene in human disease. In Protein Expression in Mammalian Cells: Methods and Protocols, expert researchers in the field present a compendium of vital techniques to further our knowledge of mammalian protein expression. 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 tips for troubleshooting and avoiding known pitfalls. Authoritative and concise, Protein Expression in Mammalian Cells: Methods and Protocols will aid scientists seeking to delve deeper into our own biology through the medium of other mammalian cells and proteins.

Super secondary structure(SSS) helps to understand the relationship between primary and tertiary structure of proteins. In Protein Supersecondary Structure: Methods and Protocols expert researchers in the field detail the usefulness of the study of super secondary structure in different areas of protein research. This is done through four main studies SSS representation, SSS prediction, SSS and protein folding, and other application of SSS concept to protein biology. 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 Supersecondary Structure: Methods and Protocols highlight some of the major advances in the many fast-growing areas of supersecondary structure research.

The understanding of the events taking place in a cell, a biological fluid or in any biological system is the main goal of biology research. Many fields of research use different technology to assess those events. Mass spectrometry is one of those techniques and this undergoes constant evolution and adaptation to always enhance the accuracy of the information provided. Proteomics provides a large panel of data on protein identity and protein expression that were made possible by mass spectrometry. For several years now mass spectrometry has become central to performing proteomic research, however this powerful tool is under constant evolution to be more sensitive and more resolute. More importantly mass spectrometry became a field of research focusing on new applications. Indeed, the complexity in biological systems relies on the changes of expression of transcription of proteins but also on the post-translational modification of proteins, the structure of proteins and the interaction between proteins, amongst others. As of now, several investigations tried to improve the quantification of proteins by mass spectrometry, the determination of post-translational modifications, the protein-protein and protein-nucleic acids interaction or the proteins structures. This book is structured as follows: after a brief introduction of the usual and most popular applications for mass spectrometry in proteomics, the most recent research and developments in mass spectrometry-based methodologies will be explored.

For design purposes one needs to relate the structure of proposed materials to their NLO (nonlinear optical) and other properties, which is a situation where theoretical approaches can be very helpful in providing suggestions for candidate systems that subsequently can be synthesized and studied experimentally. This brief describes the quantum-mechanical treatment of the response to one or more external oscillating electric fields for molecular and macroscopic, crystalline systems. To calculate NLO properties of large systems, a linear scaling generalized elongation method for the efficient and accurate calculation is introduced. The reader should be aware that this treatment is particularly feasible for complicated three-dimensional and/or delocalized systems that are intractable when applied to conventional or other linear scaling methods.

This book offers comprehensive information on the polymorphisms of genes encoding pattern recognition receptors (PRRs). Following a short description of the general role of PRRs in the immune system, the structure and function of Toll-like and NOD-like receptors are examined in detail. The main focus is on the role of inherited variation in PRRs and their correlation to cancer and cardiovascular diseases. A review of all epidemiological investigations is included, and a concept of genomic risk markers for the prevention of various diseases is also discussed.

Although phosphorylation of proteins on tyrosine is relatively rare compared to phosphorylation on serine or threonine residues, the past two decades of research into PTP function have led to a great appreciation of the critical role PTPs have in regulating basic cellular processes. Among these important roles is the regulation of cellular signaling pathways related to metabolism. This volume contains chapters which highlight many aspects of PTP function in the context of metabolism. Given the growing obesity and diabetes epidemics in the United States and throughout the world, the desire to identify possible therapeutic targets for treatment of these diseases is a high priority. In many ways, PTPs may be attractive drug targets since they are amenable to targeting with small molecules; however many challenges abound in making PTP inhibitors.

Epigenetic modifications underlie all aspects of human physiology, including stem cell renewal, formation of cell types and tissues. They also underlie environmental impacts on human health, including aging and diseases like cancer. Consequently, cracking the epigenetic "code" is considered a key challenge in biomedical research. Chromatin structure and function are modified by protein complexes, causing genes to be turned "on" or "off" and controlling other aspects of DNA function. Yet while there has been explosive growth in the epigenetics field, human chromatin-modifying machines have only recently started to be characterized. To meet this challenge, our book explores complementary experimental tracks, pursued by expert international research groups, aimed at the physical and functional characterization of the diverse repertoire of chromatin protein machines - namely, the "readers, writers and erasers" of epigenomic marks. These studies include the identification of RNA molecules and drugs that interact selectively with components of the chromatin machinery. What makes this book distinctive is its emphasis on the systematic exploration of chromatin protein complexes in the context of human development and disease networks.

Christopher M. Cheatum and Amnon Kohen, Relationship of Femtosecond-Picosecond Dynamics to Enzyme-Catalyzed H-Transfer. Cindy Schulenburg and Donald Hilvert, Protein Conformational Disorder and Enzyme Catalysis. A. Joshua Wand, Veronica R. Moorman and Kyle W. Harpole, A Surprising Role for Conformational Entropy in Protein Function. Travis P. Schrank, James O. Wrabl and Vincent J. Hilser, Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations. Buyong Ma and Ruth Nussinov, Structured Crowding and Its Effects on Enzyme Catalysis. Michael D. Daily, Haibo Yu, George N. Phillips Jr and Qiang Cui, Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Karunesh Arora and Charles L. Brooks III, Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase. Steven D. Schwartz, Protein Dynamics and the Enzymatic Reaction Coordinate.