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The second edition of the textbook Enzymes- Catalysis, Kinetics, and Mechanisms focuses on the two broad mechanistic facets of enzymology namely, the chemical and the kinetic. It endeavors to bring out the synergy between enzyme structures and mechanisms. Written with a self-study approach in mind, the emphasis is on how to begin experiments with an enzyme and subsequently analyze the data. The book is divided into six major sections– 1) Enzyme Catalysis – A Perspective, 2) Enzyme Kinetic Practice and Measurements, 3) Elucidation of Kinetic Mechanisms, 4) Chemical Mechanisms and Catalysis, 5) Exploiting Enzymes, and 6) An end piece on Frontiers in Enzymology. The individual concepts are treated as stand-alone short sections. In case the reader needs to use any one concept, it should be possible with minimal cross-referencing to the rest of the book. Further, the book presents specialized techniques and complex approaches that require involved experimentation in theory with suitable references to guide the reader. The book is proposed more as a textbook in a self-learning mode to students of modern biology, particularly those with limited exposure to quantitative aspects and organic chemistry.

The second edition of this book provides a completely updated account of the structure, dynamics, and physics of viral particles: from the moment they emerge by self-assembly from viral components produced in the infected cell, through their extracellular stage, until they recognize and infect a new host cell and cease to exist as they lose their physical integrity to initiate a new infectious cycle. New insights into the structure of viruses, their physical properties, and mechanisms of action, derived from results obtained in the last decade, have been included, as well as other (bio)physical techniques to study the structure or dynamics of virus particles and components. These include, among many others, new advances in high-resolution electron cryomicroscopy; novel approaches in the use of electron cryotomography or the application of soft X-ray tomography to study viruses in the infected cell; high-speed atomic force microscopy to study virus assembly and dynamics; and the development of new antiviral drugs and vaccines. as well as of many nanomedical and nanotechnological applications of virus particles. New chapters on the study of viruses inside infected cells and on technological applications of modified viral particles have been included in this second edition. The book is still aimed primarily at Master's students, Ph.D. students, and postdoctoral researchers with degrees in biology, chemistry, physics or related scientific disciplines who have an interest in or are working with viruses. It provides an up-to-date overview of many important concepts, techniques, studies and applications in structural and physical virology for specialized researchers working with viruses, regardless of their field of specialization, covering the latest research together with fundamental concepts and well-established facts. In short, this book is basic enough to be used by undergraduate and Ph.D. students, but advanced and up-to-date enough for experienced scientists with an interest in structural and/or physical virology.

This volume in the Subcellular Biochemistry (SCBI) series is a continuation of several previous volumes devoted to the structural and functional study of protein complexes. The expanding nature of this field of study, derived mainly from X-ray crystallography and electron cryomicroscopy, justifies the continuing expansion of coverage in an almost encyclopaedic manner within the SCBI series. Experienced and active researchers in the field shed light on the biology of protein complexes involved in important cellular functions from different perspectives, such as AcrAB-TolC, and CST. Other topics covered are: the Toxin-Antitoxin systems in cell survival, the role of the ATPases CueR and RUVBL1-RUVBL2 in the regulation of gene expression, complexes with multiple functions in the cell such as VCP/p97 or the Vault complex, FtsA and FtsZ in bacterial cell division, GATOR1 and GATOR2 in amino acid sensing, TRPA1 and the Serotonin Transporter in signaling, oligomeric structures in eukaryotic cells such as amyloids and invertases, among others. The book is richly illustrated, the result of an impressive integration of structural data from X-ray crystallography and cryo-electron microscopy. Functional aspects of protein-protein interactions are also featured prominently, providing a valuable contribution for researchers and scholars. Chapter 13 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

The second edition of this book presents the role of osmolytes in human health and diseases. Some of the chapters deal about the possibility of the use of osmolytes as diagnostic biomarkers and potential drug design for neurodegenerative and other human diseases. Other chapters also include reviews on the role of osmolytes in cancer, metastasis, infectious diseases, metabolic disorders, immunological disorders, and tissue regeneration. Importantly, the book also contain recent updates on the role of naturally occurring osmolytes in protein folding pathway, protein stability, and their underlying mechanisms. The book also covers the aspects that osmolytes could promote conformational alterations of transcription factors that favor metastatic behavior. Potential of the osmolytes in the various process of vaccine development, including enhancing the efficacy, production, and purification steps are also succintly described. Towards the end, the book also elucidates the use of specific molecules for the prevention of toxic gain of functions and restoration of function to disease-causing mutant protein. This book is an invaluable asset for the researchers especially working in osmolyte biology and scientists involved in basic and clinical research particularly neurodegeneration, diabetes, cancer, and metabolic disorders.

This book serves as a comprehensive summary of the priority program SPP 1934, which focused on understanding the dispersity, structure, and phase changes of proteins and bio-agglomerates in biotechnological processes. Through contributions from various research groups, the program explored how sensitive proteins and bio-agglomerates are affected by the process environment during fermentation, downstream processing, and formulation. It investigated these effects across three size scales: microscale, encompassing single proteins, clusters, crystals, and virus-like particles; mesoscale, focusing on cells and cell clusters; and macroscale, examining overall process dynamics. The main objective was to enhance biotechnological process chains by elucidating the mechanical, thermal, and chemical stresses that impact protein and bio-agglomerate structures. By gaining insights into these stressors, the program aimed to enable precise control measures to mitigate denaturation and unfavorable growth of proteins and cells. This compilation seeks to contribute to the optimization of biotechnological processes, facilitating advancements in various industries.

This book provides an up-to-date overview of key areas of ageing research with a special focus on anti-ageing intervention strategies, which are currently very much at the forefront of ageing studies.The volume discusses how dietary restriction, supplements or exercise affect the ageing process. Other intervention strategies reviewed are: chaperone activators, telomerase activation, hormetics, senolytics, NAD boosting, geroprotectors, stem cell therapies, resveratrol and melatonin, to just name a few. This book follows on from Parts I-IV of Biochemistry and Cell Biology of Ageing within the Subcellular Biochemistry book series and highlights anti-ageing intervention strategies that were not included in the earlier volumes. Comprehensive and cutting-edge, this book is a valuable resource for experienced researchers and early career scientists alike, who are interested in learning more about the fascinating and challenging question of why and how our cells age.

This thesis illuminates the critical roles biomolecules, from small molecules to proteins, play in cellular functionality, particularly highlighting their conformational changes in response to environmental cues or binding events—a cornerstone concept in drug design as well as the manifestations of disease. It explores the conformational flexibility of small molecules and proteins, essential for predicting drug interactions and understanding biological processes. Through advanced molecular dynamics simulations and enhanced sampling techniques, this research offers unprecedented insights into the structural dynamics of three distinct biomolecular systems: the capsid assembly modulator AT130, the passenger domain of pertactin, and the SARS-CoV-2 spike protein. Each system represents a unique facet of biological complexity, underscoring the thesis's contribution to our understanding of biomolecular behavior across various scales. Furthermore, the thesis advances the field by updating the Force Field Toolkit for improved simulation accuracy. This work not only showcases the adaptability and importance of simulation techniques in modern biological research but also paves the way for novel therapeutic strategies by deepening our understanding of biomolecular dynamics.

Amino Acids, Peptides and Proteins is a broad ranging title comprising a selection of comprehensive and critical reviews of significant developments at the biology and chemistry interface. Compiled by leading researchers in their subject, this volume incorporates current trends and emerging areas reflecting the state-of-the-art research in this field. Appealing broadly to researchers in academia and industry, it will be of great benefit to any researcher wanting a succinct reference in this field and looking at the future.

The book reviews cutting-edge advancements and their implications across various domains of molecular diagnostics. It covers foundational topics like protein-ligand interactions, lipid-protein interactions within biological membranes, and the application of NMR spectroscopy in understanding membrane structures. The book also explores advanced techniques such as X-ray crystallography, liposome microarray assays, and protein-lipid interaction studies. By integrating experimental and computational methods, it provides a comprehensive guide to understanding the complexities of molecular diagnostics, from basic principles to innovative approaches in drug discovery and therapeutic development. Each chapter offers detailed discussions on specific topics, supported by experimental data and methodological insights, making it an invaluable resource for researchers, clinicians, and students seeking to enhance their knowledge and expertise in molecular diagnostics.

This book brings out a comprehensive collection of information on the structural proteins of fish in both marine and fresh water system. The main focus of this book is to address all relevant aspects of structural proteins of fish and its commercial significance. Fish is a rich and cheap source of protein, and the collagen and myofibrillar proteins, play a key role in food and pharmaceutical industries. Marine-based collagen due to its unique properties have fewer risks of transmitting diseases. These have low molecular weight, are biocompatible, lack religious constraints, and involves cost-effective extraction process. Therefore, it finds wide biomedical applications. The details of its extraction, isolation and characterization, supported with photographs and flow-charts are provided. This book also discusses the different peptides and derivatives of proteins that may have beneficial health significance and other commercial importance. Further, the application of bioinformatics and artificial intelligence in understanding the protein structure in-silico are also discussed in detail. This book is of interest and useful to students, academician, researchers and industrialists/ entrepreneurs, and is a valuable source of reference to the relevant researchers/ students.

COVID-19 has brought us extensive research databases in the fields of biophysics, biology, and bioinformatics. To extract valuable structural bioinformatic information of SARS-CoV-2 structural and nonstructural proteins, it is necessary to work with large-scale datasets of molecular dynamics (MD) trajectories that need to be optimized. This monograph serves as a comprehensive guide to optimization-based MD studies of the molecular structures of SARS-CoV-2 proteins and RNA. The book begins by performing local optimization, taking into account the three-body movement and optimizing the noncovalent bonds of each molecular structure. The optimized structures reach a transition state that offers the best stability and lowest energy. The optimization process utilizes a hybrid strategy that combines mathematical optimization with various local search algorithms. This approach significantly reduces data volume while eliminating irrelevant bioinformatics data. To gain a thoroughunderstanding of molecular stability and the mechanism of action, it is essential to consider not only static NMR, X-ray, or cryo-EM structures but also dynamic information obtained through MD or Quantum Mechanics/Molecular Mechanics (QM/MM) simulations. These simulations capture the internal motions and dynamic processes of molecules. Furthermore, for each protein, the structural bioinformatics obtained from the optimized structure is validated by analyzing large-scale MD trajectory databases, which are openly and freely available online. The analysis includes key structural bioinformatics aspects such as salt bridge electrostatic interactions, hydrogen bonds, van der Waals interactions, and hydrophobic interactions specific to each SARS-CoV-2 molecular structure. The book also delves into discussions on drugs, vaccines, and the origins of the virus. Additionally, pandemic mathematical models, including those incorporating time delays, are explored. This book is particularly valuable for professionals working in practical computing roles within computational biochemistry, computational biophysics, optimization and molecular dynamics, structural bioinformatics, biological mathematics, and related fields. It serves as an accessible introduction to these disciplines and is also an excellent teaching resource for students.

Regulation of Downstream Targets, Volume 134 in the Advances in Protein Chemistry and Structural Biology series, presents interesting chapters on topics such as Transcriptional regulatory mechanisms and signaling networks in Viral Infections, Identification of potential key genes associated with pathogenesis and prognosis of endometrial cancer based on Integrated Bioinformatics Approaches, Differential regulation of genes in stage IB pancreatic cancer associated with increased risk of metastasis, AMPK-related LKB1-downstream targets, A compilation of bioinformatic approaches to identify novel downstream targets for the detection and prophylaxis of cancer, Protein phosphatases and their targets: Critical determinants of signaling pathway in plants, and more. Other sections cover Calcium decoders and their targets: The holy alliance that regulate cellular responses, Importin alpha family NAAT/IBB domain: functions of a multi-faceted long chameleon sequence, Aurora Kinase A and related downstream molecules: A Potential Network for Cancer Therapy, Emerging Role of Heat Shock Proteins in Cardiovascular Diseases, Function, Structure, Evolution, Regulation and Drug Target Relevance of Arylalkylamine N-acetyltransferase, and Analysis of signaling cascades from myeloma cells treated with pristimerin. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in the Advances in Protein Chemistry and Structural Biology series - Updated release includes the latest information on the Regulation of Downstream Targets

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.​

Molecular self-assembly has been exploited by nature for developing the higher functional macromolecular structures of both the genome and proteome. Inspired by nature, there has been a surge of research, in the last two decades, for the molecular engineering of peptide-based self-assembling nanostructures, adopting the bottom-up design approach. This book gives the reader an overview on the design rules for de novo self-assembling peptide and reviews the diverse range of bioinspired peptide nanostructures such as β-sheet and β-hairpin, α-helical and coiled coil, self-assembling short peptides and peptidomimetics, collagen-based and elastin-like peptides, silk peptides, peptide amphiphiles, peptides co-polymers and others. The book also covers the wide variety of responsive and functional biomaterials that have been innovated based on those nanostructures for various applications ranging from tissue engineering, therapeutics and drug delivery to antimicrobial nanomaterials and biosensors. Finally, the book also discusses the peptide bionanomaterials global market and the future of the emerging industry.Chapter “Characterization of Peptide-Based Nanomaterials” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This book aims to provide scientific information about proteins. 28 chapters have been written that describe the characteristics of proteins and their influence on human physiology. The authors presented the structure of individual proteins and their role in particular diseases. Proteins are among the most important nutrients responsible for the proper functioning of the body. Protein is one of the basic building blocks of our tissues and plays a role in transport, regulating biochemical processes and in reactions initiated by the immune system.

Cholesterol is an essential component of the plasma membrane. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), although a minor phospholipid, is the most abundant membrane phosphoinositide. Both lipids play key roles in a variety of cellular functions including as signalling molecules and major regulators of protein function. Studies on these important lipids have traditionally focused on the effect of each lipid individually. Accumulating evidence indicates, however, that these lipids may cross-regulate each other's levels. Furthermore, it is becoming evident that cholesterol and PI(4,5)P2 can act together to modulate protein function and biological processes. This book provides an overview of cellular functions and molecular mechanisms in which cholesterol and PI(4,5)P2 functions extend from parallel existence to crosstalk. It includes four sections. The first section introduces the reader to cholesterol and PI(4,5)P2. The second section demonstrates the mutual influence of these two critical lipids on their levels. The third section, divided into two parts, describes the co-modulation of protein function by cholesterol and PI(4,5)P2. The first part focuses on ion channels and the second - on lipid transfer proteins. The fourth section highlights other cellular processes at the intersection of cholesterol and PI(4,5)P2 involvement. Collectively, the book portrays the emerging relationship between cholesterol and PI(4,5)P2 in a broad array of biological systems and processes. The book will be of interest to a wide audience of research scientists with an interest in the biophysical properties of lipids and the physiological consequences of their presence in biological systems, as well as graduate students, postdoctoral trainees, basic and clinical researchers, and pharmaceutical scientists. Specifically, the content will be relevant to researchers in the fields of biochemistry, molecular biophysics, pharmacology, neurobiology, cardiovascular biology, among others.Provides a comprehensive overview of the current knowledge of the interplay between cholesterol and PI(4,5) P2Provides an overview of the emerging relationship between cholesterol and PI(4,5)P2 in biological systems and processesDiscusses cellular processes and molecular mechanisms where lipid functions extend from parallel existence to crosstalk

This updated and expanded volume gives new insights on ferroptosis – an iron-dependent form of non-apoptotic cell death. The collection of chapters discusses the two major pathways through which ferroptosis can occur: the extrinsic or transporter-dependent pathway and the intrinsic or enzyme-regulated pathway.Readers will gain an understanding of the multiple levels, on which this special cell death is regulated. Hence, the contributions will take a closer look at epigenetic, transcriptional, posttranscriptional and posttranslational layers. Among the described regulators and transcription factors are GPX4, ACSL4 and NFE2L2. This edited volume collects reviews related to current knowledge on the integrated molecular machinery of ferroptosis, thereby also describing how dysregulated ferroptosis is involved in human diseases.

This book aims to provide scientific information about proteins. 30 chapters have been written that describe the characteristics of proteins and their influence on human physiology. The authors presented the structure of individual proteins and their role in particular diseases. Proteins are among the most important nutrients responsible for the proper functioning of the body. Protein is one of the basic building blocks of our tissues, plays a role in transport, regulating biochemical processes and in reactions initiated by the immune system.

Modifications and Targeting of Protein Termini, Volume 684 in the Methods in Enzymology series serial highlights new advances in the field, with this new volume presenting interesting chapters pn a variety of timely topics, including Optimizing purification and activity assays of N-terminal methyltransferase complexes, In vitro reconstitution of hierarchical steps of Arg/N-degron pathway, Identification of N-degrons and N-recognins by using peptide-pull-downs combined with quantitative proteomics, A decoupled Virotrap approach to study the interactomes of N-terminal proteoforms, Monitoring ADO-dependent proteolysis in cells using fluorescent reporter proteins, Site-specific α-N-terminal methylation on peptides through chemical and enzymatic methods, and more. Additional sections cover Monitoring the interactions between N-degrons and N-recognins of the Arg/N-degron pathway, Characterization and chemical modulation of p62/SQSTM1 as an autophagic N-recognin of the Arg/N-degron pathway, Analysis of higher plant N-degron pathway components and substrates via expression in S. cerevisiae, and so much more. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in the Methods in Enzymology serials - Updated release includes the latest information on Modifications and Targeting of Protein Termini

This book highlights the different aspects of the research project “E4C Horizon 2020 European Project” aimed at fighting the coronavirus by combining the best supercomputing resources and artificial intelligence with state-of-the-art experimental facilities up through clinical validation. Coronavirus disease has become an important public issue across the globe since December 2019. There is an urgent need to develop potent anti-COVID-19 agents for the prevention of the outbreak and stop viral infections. To this aim, a public–private consortium composed by European and national infrastructures, center of excellence, universities, and a pharmaceutical company started the E4C Horizon 2020 European Project: Its core idea was to use the EXaSCale smArt pLatform Against paThogEns (EXSCALATE) supercomputing platform for a process known as “drug repurposing”, namely to identify the most promising safe in man drugs for immediate treatment of the already infected population and then novel pan-coronavirus inhibitors to address future emergencies. This ambitious goal exploited a “chemical library” of 500 billion molecules, thanks to a processing capacity of more than 3 million molecules per second, made available by the computing power of the EXSCALATE platform.