Protein Design: Method and Applications, Second Edition expands upon the previous edition with current, detailed ideas on how to approach a potential protein design project. With new chapters on metals as structure-forming elements and functional sites, the design and characterization of fluorinated proteins, top-down symmetric deconstruction and the design of protein libraries and novel or repurposed enzymes. Written in the highly successful Methods in Molecular Biologyseries 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. Thorough and intuitive, Protein Design: Method and Applications, Second Edition provides a number of practical protocols and instructive reviews to aid in the creation of new experiments.

Get Insight on the Function of Supercomplexes in Biological Systems Redox Proteins in Supercomplexes and Signalosomes is one of the first books to explore the key role played by redox proteins and their interaction network in a wide range of essential cellular processes in all domains of life. The book explains how the mitochondrial respiratory chain is dynamically organized in supercomplexes even under physiological conditions. It also addresses the impact of supercomplex assembly on mitochondrial morphology, physiology, and biogenesis to shed light on the molecular mechanisms of pathological situations, including aging. Discover the Connection between Bioenergetic Supercomplexes and Signalosomes Compiling state-of-the-art research from leading practitioners in the field, this book gives you guidance on dealing with these biological systems in your investigations. The book shows that supercomplexes and signalosomes provide the link between reductive and systems biology, which enables us to understand how the molecular properties of individual macromolecular components trigger cellular function.

Protein targeting is a fast-moving field that has encompassed areas from biophysics to molecular biology to try to gain insight into how proteins are directed to their final functional location and how such macromolecules are able to cross semi-permeable membrane barriers during their journey. This text reviews our current state of knowledge regarding the interaction of proteins at the membrane interface and the assembly of proteins into biological membranes, before proceeding to look at targeting pathways in both prokaryotic and eukaryotic systems. The reviews have been written by some of the leading researchers in the field, with contributions from around the world and with more than 1,800 references. The text is aimed at graduate students and at researchers with an interest in protein targeting, but may also be of use to final-year undergraduates.

Originally published in 1998.

The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These paperback editions preserve the original texts of these important books while presenting them in durable paperback editions. The goal of the Princeton Legacy Library is to vastly increase access to the rich scholarly heritage found in the thousands of books published by Princeton University Press since its founding in 1905.

The ?eld of sensory science has grown exponentially since the publication of the p- vious version of this work. Fifteen years ago the journal Food Quality and Preference was fairly new. Now it holds an eminent position as a venue for research on sensory test methods (among many other topics). Hundreds of articles relevant to sensory testing have appeared in that and in other journals such as the Journal of Sensory Studies. Knowledge of the intricate cellular processes in chemoreception, as well as their genetic basis, has undergone nothing less than a revolution, culminating in the award of the Nobel Prize to Buck and Axel in 2004 for their discovery of the olfactory receptor gene super family. Advances in statistical methodology have accelerated as well. Sensometrics meetings are now vigorous and well-attended annual events. Ideas like Thurstonian modeling were not widely embraced 15 years ago, but now seem to be part of the everyday thought process of many sensory scientists. And yet, some things stay the same. Sensory testing will always involve human participants. Humans are tough measuring instruments to work with. They come with varying degrees of acumen, training, experiences, differing genetic equipment, sensory capabilities, and of course, different preferences. Human foibles and their associated error variance will continue to place a limitation on sensory tests and actionable results. Reducing, controlling, partitioning, and explaining error variance are all at the heart of good test methods and practices.

Glycans play essential roles in diverse biological and etiological processes and their structural complexity endow various functions. The glycome is the entire set of glycans produced by an individual organism. As the glycan microarray emerged, a good amount of knowledge has been obtained in understanding the functions of glycans. However, limited accessibility of glycans is a major obstacle to the functional glycomics study. Although isolation from biology samples provided some structures, the low abundance of glycans obtained and the difficulty in complete structural assignment restricted the subsequent assay. To circumvent this limitation, many synthetic strategies, including chemical, enzymatic and chemo-enzymatic ones have been developed to make libraries of structurally defined complex glycans available. The glycans provided by these techniques combined with high-throughput glycoarray techniques have broadened and deepened our understanding about functional glycomics. The aim of this book is to provide a comprehensive review of the current state of the synthetic glycome and a brief introduction of the application of the synthetic glycome in glycoarray assay. Accordingly, synthetic strategies toward generating glycans with comprehensive structures as well as the glycoarrays to unveil the glycan functions are described in this book.

Advances in fluorescent proteins, live-cell imaging, and superresolution instrumentation have ushered in a new era of investigations in cell biology, medicine, and physiology. From the identification of the green fluorescent protein in the jellyfish Aequorea victoria to the engineering of novel fluorescent proteins, The Fluorescent Protein Revolution explores the history, properties, and applications of these important probes. The book first traces the history of fluorescent proteins and the revolution they enabled in cellular imaging. It then discusses fluorescent proteins with novel photophysical properties. The book also covers several cutting-edge imaging applications. These include superresolution microscopy of cellular fine structures, FRET microscopy to visualize protein interactions and cell-signaling activities inside living cells, photobleaching and photoactivation techniques to visualize protein behaviors, techniques that exploit plant and algal photoreceptors to enable light-regulated control of enzymatic activities, and the noninvasive imaging of tumor-host interactions in living animals. In color throughout, this book presents the fundamental principles and latest advances in the field, including the associated development of imaging techniques that exploit fluorescent proteins. It is accessible to a broad audience, from optical imaging experts to novices needing an introduction to the field.

Electrochemical Analysis of Proteins and Cells presents the remarkable progress made over the years in the electrochemical analysis of proteins and cells, due to the rapid development of protein electrochemistry together with related technologies such as surface modification, molecular recognition, molecular assembly, and nanotechnology. As an interdisciplinary field combining electrochemistry, analytical chemistry, biochemistry, biophysics, biomedicine and material science, the electrochemical analysis of proteins and cells has attracted broad and extensive research interest. The main emphasis of this book is on the principles of electrochemical strategies and the practical utility of related detection systems, which is of great importance in all biological sciences, such as cell biology and molecular biology, as well as in biomedical fields like cancer research. This brief offers an up-to-date, easy-to-follow presentation of recent advances on the subject and can serve as a supplement for graduate-level courses in analytical chemistry, biochemistry, biophysics, biotechnology, biomedical engineering, etc. It may also help young scientists get an overview of this topic.

Take the guesswork out of keto meal prep planning with over 60 low-carb recipes and 8 easy-to-follow weekly meal plans! Eating keto can be challenging, and cooking keto recipes that are satisfying can be even more challenging--you need to make sure you're eating enough fat to stay in ketosis, while still eating food that is satisfying. Weekly meal prep can help ensure that you stay in ketosis while still enjoying fresh, delicious, keto-friendly recipes that aren't the same every week. With Easy Keto Meal Prep, planning and preparing your weekly keto meals has never been easier! Here's what you'll find inside: - 8 weekly meal plans, each with a detailed step-by-step prep plan, shopping list, and equipment list, and each with four main recipes and four alternative recipes that can be swapped in - Over 60 delicious recipes, each with specific macros and detailed nutrition information to ensure you're always eating the right ratios to stay in ketosis. - Beautiful photography and visual meal grids that show you exactly what you'll be eating each day, along with the macros ratios for each day's meals - Helpful guidance for eating keto, sticking with the diet, meal prepping like a pro, and safely storing your prepped meals

Neutron Protein Crystallography is one of the first books dedicated to the emerging field of neutron protein crystallography (NPC). The text covers all of the practical aspects of NPC, from the basic background of neutron scattering and diffraction, to the technical details of neutron facilities, growth of high-quality crystals, and data analysis. The final chapter is devoted to providing many examples of using NPC to investigate a wide range of different proteins. It demonstrates how NPC can explore hydrogen bonds, protonation and deprotonation of amino acid residues, hydration structures, and hydrogen-to-deuterium exchange ratios.
To avoid redundancy with other textbooks on X-ray protein crystallography (XPC), this book assumes a familiarity with the basics of XPC and strives to highlight and explain the differences between XPC and NPC. It is therefore especially useful for X-ray protein crystallographers who are eager to have a sound, scientific basis for judging if NPC is the right technique for furthering their experimental programs.

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

Despite being known and studied for years, peptides have never before attracted enough attention to necessitate the invention of the term "peptidomics" in order to specify the study of the complement of peptides from a cell, organelle, tissue or organism. In Peptidomics: Methods and Protocols, expert researchers present a comprehensive range of analytical techniques for the analysis of the peptide contents of complex biological samples with an emphasis often on higher throughput techniques, suitable for the analysis of large numbers of peptides typically present in the peptidomes. Encompassing a number of species ranging from bacteria to man, the methods presented intensively cover topics such as organism handling, tissue and organ dissection, cellular and subcellular fractionation, peptide extraction, fractionation and purification, structural characterization, molecular cloning, and sequence analysis. 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 notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Peptidomics: Methods and Protocols brings this ten year old field fully up-to-date in order to inspire novices and experts alike with the easy-to-follow practical advice needed to set up and carry out analysis of the peptide contents of complex biological samples.

Familiar sciences of biology, physics, chemistry, cybernetics, and computational methods for dealing with vast new data sets of information at molecular and sub-molecular levels are morphing into new sciences. Some exist beneath our line of sight where laws of nature hover between Newtonian and quantum mechanics. New fields of cyber-, bio-, nanotechnology and systems biology raise arcane new concepts. The completed human genome has led to an explosion of interest in genetics and molecular biology. The view of the genome as a network of interacting computational components is well established and here writers explore it in new ways. These systemic approaches are timely in light of the availability of an increasing number of genomic sequences, and the generation of large volumes of biological data by high-throughput methods. Suitable for two-semesters of study, the works surveys genomics principles in the 13 chapters of Vol I, and networks and models in the 14 chapters of Vol II. Both, as a two-book set, will serve as core foundation titles for Dennis Shasha's Series in Systems Biology, establishing the principles and challenges for this emerging field of study. In each chapter world-renowned experts trail-blazing in their respective fields will review corresponding topics as well as current and planned research. Chapters will treat the integrated study and analysis of biological systems by use of data and information about the system components in their entirety, as opposed to the study of individual components in isolation. Systems Biology courses are popping up all over the place and biology, computer science, and bioinformatics programs are the primary potential takers. The editors plan books for a very wide audience, at the same time providing a comprehensive repository of up-to-date overviews and predictions for a number of inter-related sub-fields within this hierarchy. Intended readers include graduate students plus academic and professional researchers of genomics, bioinformatics, molecular biology, biochemistry, bioengineering, and computer systemic approaches to those fields. By comparison, Shasha's first Systems Biology Series title, Amos's Cellular Biology, is a book for technologists using biology as a vehicle to do something else, whereas this is a book about systems and related technologies in service to biologists. The volume editors plan to review or have reviewed, and to edit the invited chapters for content and consistent conceptual level, each chapter contributing uniquely to the key aspects of the Systems Biology hierarchy. A few chapter contents may date after two years, but the majority will endure for longer-term reference use because they treat methodologies and provide sample applications.

TLR4 is one of the most important innate immunity receptors, its function mainly consisting in the activation of inflammatory pathways in response to stimulation by Pathogen-Associated Molecular Patterns (PAMPs) and Damage Associated Molecular Pattern molecules (DAMPs). This volume critically reviews the different types of TLR4 activators and inhibitors, discusses the role of molecular aggregates in agonism/antagonism as well as the pivotal role of the CD14 receptor in the modulation of TLR4 signal and the molecular details and actors of the intracellular cascade. The book presents the role of TLR4 in several pathologies, such as sepsis and septic shock caused by receptor activation by gram-negative bacterial lipopolysaccharide (LPS), in neurodegenerative and neurological diseases such as Parkinson and Alzheimer's diseases, and Amyotrophic Lateral Sclerosis (ALS). It reviews the role of TLR4 in neural stem cell-mediated neurogenesis and neuroinflammation and in Human Induced Pluripotent Stem Cells and Cerebral Organoids and discusses the emerging role of micro-RNA (miRNA) regulation by TLR4.

This volume serves to aid researchers working in the recombinant protein production field by describing a wide number of protocols and examples. Chapters describe recombinant protein production in different expression systems, prokaryotic and eukaryotic expression systems, purification protocols, characterization of insoluble proteins and a general overview of interesting applications of insoluble proteins. 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, Insoluble Proteins: Methods and Protocols, Second Edition aims to be a useful practical guide to researches to help further their study in this field.

The purpose of Protein-Protein Recognition is to bring together concepts and systems pertaining to protein-protein interactions in a single unifying volume. In the light of the information from the genome sequencing projects and the increase in structural information it is an opportune time to try to make generalizations about how and why proteins form complexes with each other. The emphasis of the book is on heteromeric complexes (complexes in which each of the components can exist in an unbound state) and will use well-studied model systems to explain the processes of forming complexes.

Fourier Transform Infrared microspectroscopy (FTIR) was first developed by William Coblentz in 1905 for analytical purposes. It has been established as a powerful analytical method to analyze a wide range of materials. The most convenient way to analyze the molecular structure was to prepare KBr pellets with small amount of chemical species. Currently, the development of the Universal Attenuated Total Reflectance (UATR) allows the use of ZnSe-Diamond crystal to acquire FTIR spectra directly from the sample with no special preparation. These traditional FTIR analyses have been made with devices capable of performing single measurements, thus, providing a single IR spectrum of the sample. Recent major technological development in FTIR instrumentation was development of microscopes and imaging systems. These devices are now capable of imaging larger sample area, providing not only spectroscopic information but also spatial distributional information. In addition, the development of Focal Point Array (FPA) has made FTIR imaging an emerging area of chemical imaging research. The aim of this book is to summarize in a single document the research work that is being performed using UATR and IR imaging in selected emerging applications in plant materials and biological samples. This book provides the readers new knowledge, updates information, emerging applications, and understanding of the potential use of FTIR Microspectroscopy.

X-ray crystallography is the major method of determining biological structures yet the procedures involved in obtaining the required crystals are still seen as something of a black art by many molecular biologists. As with the previous edition this book will dispel this idea by providing a detailed and rational guide to obtaining crystals or proteins and nucleic acids for diffraction studies.

This book provides a broad base of knowledge of G-protein-coupled receptors. Useful at both the university and industrial levels, this book is of particular interest to those who are developing therapeutic approaches to diseases using drugs that influence receptor activation.

The reproduction and spread of a virus during an epidemic proceeds when the virus attaches to a host cell and viral genetic material (VGM) (protein, DNA, RNA) enters the cell, then replicates, and perhaps mutates, in the cell. The movement of the VGM across the host cell outer membrane and within the host cell is a spatiotemporal dynamic process that is modeled in this book as a system of ordinary and partial differential equations (ODE/PDEs). The movement of the virus proteins through the cell membrane is modeled as a diffusion process expressed by the diffusion PDE (Fick's second law). Within the cell, the time variation of the VGM is modeled as ODEs. The evolution of the dependent variables is computed by the numerical integration of the ODE/PDEs starting from zero initial conditions (ICs). The departure of the dependent variables from zero is in response to the virus protein concentration at the outer membrane surface (the point at which the virus binds to the host cell). The numerical integration of the ODE/PDEs is performed with routines coded (programmed) in R, a quality, open-source scientific computing system that is readily available from the Internet. Formal mathematics is minimized, e.g., no theorems and proofs. Rather, the presentation is through detailed examples that the reader/researcher/analyst can execute on modest computers. The ODE/PDE dependent variables are displayed graphically with basic R plotting utilities. The R routines are available from a download link so that the example models can be executed without having to first study numerical methods and computer coding. The routines can then be applied to variations and extensions of the ODE/PDE model, such as changes in the parameters and the form of the model equations.

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 reviews understanding of the biological roles of extracellular molecular chaperones. It provides an overview of the structure and function of molecular chaperones, their role in the cellular response to stress and their disposition within the cell. It also questions the basic paradigm of molecular chaperone biology - that these proteins are first and foremost protein-folding molecules. Paradigms of protein secretion are reviewed and the evolving concept of proteins (such as molecular chaperones) as multi-functional molecules for which the term 'moonlighting proteins' has been introduced is discussed. The role of exogenous molecular chaperones as cell regulators is examined and the physiological and pathophysiological role that molecular chaperones play is described. In the final section, the potential therapeutic use of molecular chaperones is described and the final chapter asks the question - what does the future hold for the extracellular biology of molecular chaperones?

This book covers liquid chromatography, gas chromatography and capillary electrophoresis, the three main separation techniques lately available, applied to key omic sciences, such as genomics, proteomics, metabolomics and foodomics. The fundamentals of each technique are not covered herein. Instead, the recent advances in such techniques are presented focusing on the application to omics analyses and unique aspects in each case. This volume intends to offer wide ranging options available to researchers on omics sciences, and how to integrate them in order to achieve the comprehension of a biological system as a whole. Omic sciences have been of ultimate importance to comprehend the complex biochemical reactions and related events that occurs upon a biological system. The classical central dogma of molecular biology, which states that genetic information flows unidirectionally from DNA to RNA and then to proteins, has been gradually replaced by the systems biology approach. This book presents a multidisciplinary approach that explains the biological system as a whole, where the entire organism is influenced by a variety of internal events as well as by the environment, showing that each level of the biological information flux may influence the previous or the subsequent one.

This detailed book explores the technical breakthroughs with biophysical and cell biological approaches that have advanced the study of molecular mechanisms underlying the generation and transduction of the hedgehog (HH) signal, indicating the important role of sterols in this pathway. Within its pages, the volume examines techniques involving several key protein components in this pathway, including HH, the signaling ligand; Dispatched, a HH secretion regulator; Patched, the receptor of HH; Smoothened, the signal transducer used to transduce the HH signal across the plasma membrane; and GLI, the transcription factor to turn on HH target genes. Written in the highly successful Methods in Molecular Biology series format, chapters feature 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. Authoritative and practical, Hedgehog Signaling: Methods and Protocols provides researchers in clinical and basic science with a fresh and reliable reference for analyzing HH signal transduction through cell biological, biochemical, and biophysical approaches.

This new edition describes the role of heat shock proteins in the life cycle of malaria parasites, particularly in the context of intracellular parasite stages. Thoroughly revised, this work provides a general introduction to the structural and functional features of heat shock proteins with a special focus on their role as molecular chaperones in ensuring protein quality control. The emphasis is on the heat shock protein families from Plasmodium falciparum, and their role in proteostasis and the development of malaria pathology. Moreover, the authors explore the latest prospects of targeting heat shock proteins in antimalarial drug discovery either directly or in combination therapies. Readers will experience a functional analysis of the individual families of heat shock proteins and their cooperation in functional networks, including both the parasite-resident proteome and the exportome released into host cells during intracellular stages. Subcellular and extracellular organelles such as the apicoplast and the Maurer's Clefts associated with Plasmodium species are discussed in detail. The book highlights the role of heat shock proteins in the development and function of these structures. Biochemical expertise and the inclusion of novel therapeutic solutions make this collection a unique reference for experts in heat shock protein research, parasitology and infectious diseases, cell stress, molecular biology and drug discovery. Not least, advances in malaria control will contribute to ending epidemics and ensuring healthy lives in line with the UN Sustainable Development Goals.

This volume describes methods and protocols for the fragment-based screening of proteins using Surface Plasmon Resonance (SPR). The initial chapter of the book discusses the principle of SPR for the identification of biomolecular interactions, while the subsequent chapters introduce methods for labelling proteins with different tags including, histidine and biotin tags. It also discusses techniques and factors that affect the amine and biotin-streptavidin coupling and methods to optimize the interactions. Next, it describes fragment preparation for screening in SPR and presents methods to calculate equilibrium dissociation constant (KD) and ligand efficiency (LE). It reviews techniques of next-generation injections that improve the efficiency of the characterization process over traditional SPR by determining the kinetics and affinity in a single step. Finally, the book elucidates a comprehensive yet representative description of challenges associated with the molecular interaction of proteins using SPR.