This volume provides computational methods and reviews various aspects of computational studies of protein aggregation. Chapters discuss the relationship between protein misfolding and protein aggregation, methods of prediction of aggregation propensities of protein, peptides, protein structure, results of computer simulations of aggregation, and computational simulations focused on specific diseases such as Alzheimer's, Parkinson's, and preeclampsia. 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, Computer Simulations of Aggregation of Proteins and Peptides aims to ensure successful results in the further study of this vital field.

Actin is one of the most widespread proteins in eukaryotic cells. This book and its companion ("Molecular Interactions of Actin. Actin Structure and Actin-Binding Proteins") provide an authoritative and opinionated view of the structure and function of this essential protein. Each section includes an historical perspective and a detailed commentary on actin protein chemistry, molecular and cell biology of actin. While some chapters review the body of knowledge of the subject, others contain new experimental data. This book will appeal to research scientists seeking contemporary overviews of actin-myosin interaction and actin-based regulation. Contributors include senior scientists as well as the new breed of younger scientists.

Protein Interactions as Targets in Drug Discovery, Volume 121, is dedicated to the design of therapeutics, both experimental and computational, that target protein interactions. Chapters in this new release include Trends in structure based drug design with protein targets, From fragment- to peptide-protein interaction: addressing the structural basis of binding using Supervised Molecular Dynamics (SuMD), Protein-protein and protein-ligand interactions: identification of potential inhibitors through computational analysis, Aromatic-aromatic interactions in protein-drug and protein-protein interactions, Role of protein-protein interaction in allosteric drug design within the human methyltransferome, and much more.

The Networking of Chaperones by Co-chaperones updates the current understanding of how chaperones are regulated and networked. It is a resource for those in the specialized field of cell stress and chaperones. The book will also be of interest to those in broader cross-cutting field such as cellular networks and systems biology.

This volume presents the response of the eukaryotic translational apparatus to cellular stress and apoptosis, including kinases activated through both the ERK and stress-activated pathways. It further explores two agents that inhibit protein synthesis, calcium and the immunosuppressant rapamycin. Six chapters written by leading experts in the field provide both new data and comprehensive literature reviews. Both the regulation of initiation and elongation are discussed, and the mechanisms of apoptosis are related to changes in the protein synthesis machinery.

This volume provided methods and protocols on recombinant protein production in different plant systems, downstream processing, and strategies to optimize protein expression. Chapters guide readers through recombinant protein production in important plant systems, protein recovery and purification, different strategies to optimise productivity, cloning and fusion protein approaches, and the regulation and freedom to operate analysis of plant-produced proteins. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Recombinant Proteins in Plants: Methods and Protocols aims to be useful to newcomers and experienced researchers interested in expanding their expertise in the field of plant-based protein production. Chapters 6, 8 and 17 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

RAN: AN ATYPICAL GTPASE Mark G. Rush and Peter D'Eustachio New York University School o/Medicine. Department,o/Biochemistry New York NY 10016 ABSTRACT GTPases, proteins that bind and hydrolyze GTP (guanosine triphos- phate) are critical regulators of many metabolic pathways. Although these proteins are enzymes that catalyze the hydrolysis of GTP to GDP + Pi, their primary function is not the hydrolysis of GTP per se, but rather the coupling of this hydrolysis to metabolic regulation. Such coupling is gen- erally achieved through the interaction of the GTP-bound form of the GTPase with proteins known as *effectors. Effectors are often enzymes whose activities are modulated by the GTPase. However, effectors can also be structural proteins involved in assembling intracellular macromo- lecular complexes, such as actin filaments and microtubules, as well as proteins involved in the intracellular transport of proteins and RNAs. In- deed, the subject of this anthology, the small GTPase Ran, may exert most or all of its regulatory functions by interacting with non-enzyme effectors. This property of Ran distinguishes it from other well studied GTPases, and has resulted in the elucidation of novel mechanisms of Ran action that are quite distinct from previously established paradigms of GTPase function. 1. INTRODUCTION The Ras-related nuclear protein Ran is a highly conserved (80% identity among yeasts and humans) member of the Ras superfamily of small GTP binding and hydrolyzing proteins.

Fibroblast Growth Factors, Second Edition systematically introduces readers to FGF in the fields of injury repair and regeneration, endocrinology and metabolism, structure and modification, pharmaceutics, pharmacology, FGF/FGFR inhibitor, engineering and new drug development. Fibroblast growth factors (FGFs) are secreted protein ligands that act in a paracrine or endocrine fashion to carry out their pleiotropic functions in development, tissue homeostasis and metabolism. This book covers the work from Li’s team from 2013 to 2018 and will be a primer for scientists, particularly young students entering the FGFs field with an eye on basic research and application.

This text provides an up-to-date collection of theoretical and experimental studies into protein folding, misfolding, aggregation, and stability. Additionally, issues faced during the development of protein products are illustrated. It contains an introductory chapter for readers new to the protein folding field. The book provides a thorough and clear discussion of computational approaches to understanding and modeling protein aggregation.

With insolubility proving to be one of the most crippling bottlenecks in the protein production and purification process, this volume serves to aid researchers working in the recombinant protein production field by describing a wide number of protocols and examples. Insoluble Proteins: Methods and Protocols includes chapters that describe not only the recombinant protein production in different expression systems but also different purification and characterization methods to finally obtain these difficult-to-obtain proteins. Beginning with protein production methods using both prokaryotic and eukaryotic expression systems, the book continues with purification protocols using insoluble proteins, the characterization of insoluble proteins, as well as a general overview of interesting applications of insoluble proteins. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, Insoluble Proteins: Methods and Protocols aims to provide the scientific community with detailed and reliable state-of-the-art protocols that are used in order to successfully produce and purify recombinant proteins prone to aggregate.

This volume covers various aspects of co-immunoprecipitation (co-IP) methods and its relevant use in studying protein-protein interactions (PPIs) in health and diseases of the Central Nervous System. The chapters in this book discuss topics such as using co-IP to detect G protein-coupled receptors (GPCR), receptor tyrosine kinases (RTK) and ion channels heteroreceptor complexes in brain tissue; the histoblot technique; interaction strength between synaptic proteins using COS-7; and co-IP analysis of the protein-protein interactions in the neurons of Polymita. In Neuromethods series style, chapters include the kind of detail and key advice from the specialists needed to get successful results in your laboratory. Cutting-edge and thorough, Co-Immunoprecipitation Methods for Brain Tissue is a valuable resource for any researcher interesting in learning more about this developing field.

From the basic science to potential and approved clinical applications the most recent data in the rapidly growing field of bone morphogenetic proteins (BMPs) are summarized in this topical volume. Distinguished scientists present reviews on a range of scientific topics, including biochemistry, biology, molecular biology and preclinical animal studies on spinal fusion, cartilage repair, craniofacial and dental reconstruction using BMPs, as well as approved clinical applications in human bone non-unions.

This book provides a resource not only for experts in the field, but also for undergraduate students, newcomers and clinicians worldwide, given that the use of BMPs in orthopedic reconstruction has been already approved in Europe, Australia, Canada and the USA.

This book presents an exploratory analysis based on proteomic and ionomics studies comparing the blood serum of patients with bipolar disorder (BD), healthy controls, patients with schizophrenia (SCZ), and patients with other disorders (OD) in order to identify biomarkers of BD. Bipolar disorder is a psychiatric condition that affects thousands of people worldwide. The absence of biomarkers for BD has resulted in misdiagnosis and ineffective treatment in some patients, causing additional health problems and high costs for health systems. As such, this book evaluates various strategies for sample preparation for proteomic and ionomic studies in order to simplify complex serum samples and allow the quantification of chemical species (proteins and metal ions), which are potential candidates for BD biomarkers. In addition, it describes the development of a new membrane-based methodology for extracting urine proteins to be used in biomarker discovery.

Aging is an inevitable part of life and is becoming a worldwide social, economic and health problem. This is mainly due to the fact that the increasing proportion of individuals in the advanced age category have a higher probability of developing age-related disorders, such as type II diabetes mellitus, cardiovascular disorders, sarcopenia, and neurodegenerative conditions. New therapeutic approaches are still needed to decrease or slow the effects of such diseases. Advances in -omic technologies, such as genomics, transcriptomics, proteomics and metabolomics, have significantly advanced our understanding of disease in multiple medical areas, as the analysis of multiple molecular networks has simultaneously provided a more integrated view of disease pathways. It is hoped that emerging hits from these analyses might be prioritized for further screening as potential novel drug targets for increasing the human healthspan in line with the lifespan. In turn, this will lead to new therapeutic strategies as well as drug development projects by the pharmaceutical industry. This book presents a series of reviews describing studies that have resulted in identification of new potential drug targets for age-related disorders. Much of this information has come from -omic comparisons of healthy and disease states or from testing the effects of new therapeutic approaches. Authored by experts from around the globe, each chapter is presented in the context of specific chronic diseases or therapeutic strategies. This book is designed for researchers in the areas of aging and chronic disease, as well as clinical scientists, physicians and stakeholders in major drug companies.

Proteomics is a rapidly expanding investigation platform in cardiovascular medicine. Driven by major improvements in mass spectrometry (MS) instrumentation and data analysis, the proteomics field has flourished in recent years particularly in the study of complex diseases. These recent advances are characterized by the development of quantitative MS-based methods that promoted the field from primarily identifying proteins to also providing measurements of relative changes in protein levels between different cell states. This progress is reflected in the application of proteomic techniques to vascular pathology. Vascular Proteomics: Methods and Protocols provides up-to-date methods and protocols for the analysis of arteries, cells, lipoproteins, body fluids, and metabolites, with a particular focus on MS-based methods of protein and peptide quantification. 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, Vascular Proteomics: Methods and Protocols is a representative selection of methods that can be a useful resource for experienced proteomics practitioners as well as newcomers interested in becoming acquainted with the practice of proteomic techniques for cardiovascular research.

Leading researchers are specially invited to provide a complete understanding of a key topic within the multidisciplinary fields of physiology, biochemistry and pharmacology. In a form immediately useful to scientists, this periodical aims to filter, highlight and review the latest developments in these rapidly advancing fields.

0ne 0fthe many 1mpact5 0frec0m61nant DNA techn0109y 0ver the 1a5t 15 year5 ha5 6een a 5tr0n91y refre5hed 1ntere5t 1n meth0d5 f0r the 5eparat10n and pur1f1cat10n 0f pr0te1n5.7h15 1ntere5t ha5 enc- pa55ed n0t 0n1y ana1yt1ca1 5eparat10n5, 6ut a150 5ma11- and 1ar9e-5ca1e preparat1ve meth0d5 d1rected t0 60th pure and app11ed re5earch thr0u9h0ut 610109y and 610med1c1ne. Many 0f the new 0r 5u65tant1a11y m0d1f1ed techn14ue5 deve1- 0ped have 6een rep0rted 1n the 11terature, 6ut a 5uff1c1ency 0f deta11ed pract1ca1 he1p 1n e5ta6115h1n9 the5e meth0d5 f0r the f1r5t t1me 1n a new 1a60rat0ry ha5 0ften 6een d1ff1cu1t t0 f1nd. W1th the5e pr061em5 1n m1nd, we expect that Pract1ca1Pr0te1n Chr0mat09raphy, de519ned a5 a key v01ume 1n the Meth0d5 1n M01ecu1ar 810109y 5er1e5, w111 pr0v1de c0nc15e pract1ca1 he1p t0 th05e carry1n9 0ut new techn14ue5 f0r the f1r5t t1me. Each chapter ha5 6een wr1tten 6y expert auth0r5 kn0wn t0 have d1rect and re9u1ar pract1ca1 exper1ence w1th the1r ch05en techn14ue5. 7he 5tructure 0feach chapter 15 de519ned t0 make 1t ea5y f0r a w0rker new t0 the meth0d t0 f0110w 1t t0 an effect1ve c0nc1u510n. An 1nt- duct10n treat5 the the0ry 6eh1nd the meth0d 6e1n9 de5cr16ed. 7he Mater1a15 and Meth0d5 5ect10n5 a110w the reader t0 prepare f0r, and then perf0rm techn14ue5 1n a rat10na1 5tepw15e manner. 7he N0te5 5ect10n5 pr0v1de the 50rt 0f6ack9r0und h1nt5 and tr1ck5 that are 50 0ften e55ent1a1 f0r 5ucce55, 6ut are rare1y rep0rted 1n the 11terature.

Systems Biology represents a new paradigm aiming at a whole-organism-level understanding of biological phenomena, emphasizing interconnections and functional interrelationships rather than component parts. The study of network properties, and how they control and regulate behavior from the cellular to organism level, constitutes a main focus of Systems Biology. This book addresses from a novel perspective a major unsolved biological problem: understanding how a cell works and what goes wrong in pathology. The task undertaken by the authors is in equal parts conceptual and methodological, integrative and analytical, experimental and theoretical, qualitative and quantitative, didactic and comprehensive. Essentially, they unravel the spatio-temporal unfolding of interacting mass-energy and information networks at the cellular and organ levels, as well as its modulation through activation or repression by signaling networks to produce a certain phenotype or (patho)physiological response.

Starting with the historical roots, in thirteen chapters this work explores the Systems Biology of signaling networks, cellular structures and fluxes, organ and microorganism functions. In doing so, it establishes the basis of a 21st century approach to biological complexity.

From Globular Proteins to Amyloids proposes a model and mechanism for explaining protein misfolding. Concepts presented are based on a model originally intended to show how proteins attain their native conformations. This model is quantitative in nature and founded upon arguments derived from information theory. It facilitates prediction and simulation of the amyloid fibrillation process, also identifying the progressive changes that occur in native proteins that lead to the emergence of amyloid aggregations.

This volume provides methods for modern macromolecular crystallography, including all steps leading to crystal structure determination and analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Crystallography aims to ensure successful results in the further study of this vital field.

"Dancing protein clouds: Intrinsically disordered proteins in the norm and pathology" represents a set of selected studies on a variety of research topics related to intrinsically disordered proteins. Topics in this update include structural and functional characterization of several important intrinsically disordered proteins, such as 14-3-3 proteins and their partners, as well as proteins from muscle sarcomere; representation of intrinsic disorder-related concept of protein structure-function continuum; discussion of the role of intrinsic disorder in phenotypic switching; consideration of the role of intrinsically disordered proteins in the pathogenesis of neurodegenerative diseases and cancer; discussion of the roles of intrinsic disorder in functional amyloids; demonstration of the usefulness of the analysis of translational diffusion of unfolded and intrinsically disordered proteins; consideration of various computational tools for evaluation of functions of intrinsically disordered regions; and discussion of the role of shear stress in the amyloid formation of intrinsically disordered regions in the brain.

The articles in the present volume are by major contributors to our under standing of signaling pathways affecting protein synthesis. They focus pri marily on two extracellular anabolic signals, although others are included as well. Insulin is one of the best-studied extracellular regulators of protein syn thesis. Several of the known pathways for regulation of protein synthesis were elucidated using insulin-dependent systems. Regulation of protein synthesis by amino acids, by contrast, is an emerging field that has recently received a great deal of attention. The dual role of amino acids as substrates for protein syn thesis and regulators of the overall process has only recently been recognized. Since amino acids serve as precursors for proteins, one might expect that with holding an essential amino acid would inhibit the elongation phase. Surpris ingly, research has shown that it is the initiation phase of protein synthesis that is restricted during amino acid starvation. Understanding the mechanisms by which the biosynthesis of proteins is reg ulated is important for several reasons. Protein synthesis consumes a major portion of the cellular ATP that is generated. Therefore, small changes in protein synthesis can have great consequences for cellular energy metabolism. Translation is also a major site for control of gene expression, since messenger RNAs differ widely in translational efficiency, and changes to the protein syn thesis machinery can differentially affect recruitment of individual mRNAs."

Volume I highlights the association of the cellular prion protein (PrPC) with copper and zinc, the potential roles of PrPC in Alzheimer's disease and cancers, insoluble PrPC, PMCA, molecular and cellular mechanisms of PrPSc formation and clearance, possible co-factors involved in the conversion of PrPC into PrPSc, infectious and pathogenic forms of PrP, cell biology of prions, prion strains and their interference, as well as yeast prions and their inheritable and structural traits. This unique volume will take you through the fascinating chronicle of prions in mammals, yeast, and fungi.

Tea is an important non-alcoholic beverage plant of the world. Cultivation of tea is very important as it earns revenue for the tea growing nations especially the developing countries such as India. Although conventional breeding is well-established and has contributed significantly for varietal improvement of this plant and other Camellia species with ornamental value, yet applications of biotechnology are required to intervene some of the issues where conventional breeding is restricted particularly for woody plants such as tea. It is note-worthy to mention that some amounts of biotechnology works in several facets of tea and its wild species have also been done. In the present book, a state-of-the-art on various aspects of breeding and biotechnology has been complied in eight chapters. They are: i) Origin and descriptions of health benefits as well as morphological classification as first chapter, ii) Breeding and cytogenetics that comprise with various conventional approaches of varietal improvement of tea along with their genetic resources, iii) Micropropagation which deals with in-depth study of clonal propagation, iv) Somatic embryogenesis along with alternative techniques such as suspension culture, cry-preservation etc. v) Molecular breeding that deals with application of various DNA-based markers, linkage map etc., vi) Genetic transformation and associated factors, vii) Stress physiology complied with various works done in tea along with its wild relatives on abiotic as well as biotic stress, and viii) Functional genomics that describe the various works of molecular cloning and characterizations, differential gene expression, high-throughput sequencing, bioinformatics etc. Importantly, the author has made exclusive tables in most of the chapters that include the summary of the works in particular topic. In a nutshell, the book compiles the work already been done, identifies the problems, analyzes the gaps on breeding and biotechnological works of tea as well as its wild species and discusses the future scope as conclusion. Every effort has been made to include all the published works till June 2013. The book will be a useful resource for post-graduate, doctoral as well post-doctoral students working on tea as well as other woody plants. This will also be useful for the scientists working in the areas of life sciences, genomics, biotechnology and molecular biology.

The contents of this book focus on the recent investigations in molecular bi- ogywhereapplicationsoftopologyseemtobeverystimulating. Thevolumeis based on the talks and lectures given by participants of the three-month p- gram"TopologyinCondensedMatter,"whichwasheldintheMaxPlanck- stitut fur Physik komplexer Systeme, Dresden, Germany, 8May-31July 2002, under the scienti?c direction of Professors M. Kl eman, S. Novikov and - self. The aim of this program was to discuss recent applications of topology to several areas in condensed matter physics and molecular biology. The ?rst volume "Topology in Condensed Matter" is concerned with m- ern applications of geometrical and topological techniques to such new and classic ?elds of physics like electron theory of metals, theory of nano-crystals, aperiodic and liquid crystals, quantum computation and so on. This volume is published simultaneously in "Springer Series in Solid-State Physics." The present volume gives an exposition of the role of topology in the theory of proteins and DNA. The last thirty years a?rmed very e?cient - plications of modern mathematics, especially topology, in physics. The union of mathematics and physics was very stimulating for both sides. On the other hand, the impact of mathematics in biology has been rather limited. H- ever here also some interesting results were obtained. In particular, there are applications of knot theory in the theory of circular closed DNA. The - cent discoveries in molecular biology indicate future successful applications of topology."