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This volume looks at the latest methods used to study and modulate the biological function and mechanisms of SH2 domains. The chapters in this book are organized into five parts. Part One presents methodology aimed at determining the structures and dynamics of SH2 domains and their complexes with phosphopeptides. Part Two discusses techniques to understand and predict interactions of SH2 domains by measuring or calculating their affinity to phosphopeptides. Part Three focuses on inhibitors of SH2 domains that lead the way for chemical tool development and drug discovery. Part Four describes how to evolve and engineer SH2 domains with specific binding properties, and Part Five explores how to measure the regulation of protein tyrosine phosphatase activity through allosteric binding of peptides to SH2 domains and condensation. 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. Cutting-edge and comprehensive, SH2 Domains: Functional Modules and Evolving Tools in Biology is a valuable resource for researchers, working in the biophysical and biochemical field, who want to learn more about this exciting and versatile class of regulatory and signaling domains. .
Cytology. --- Biomolecules. --- Physical biochemistry. --- Macromolecules. --- Proteins. --- Cell Biology. --- Structural Biology.
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DNA damage response (DDR) and lesion repair are vital processes ensuring genome integrity through various pathways depending mainly on the nature of DNA injury and cell cycle stage. DDR is finely regulated at many levels in co-ordination with other ongoing processes as is genome replication and cell cycle progression. Posttranslational modifications (PTMs), affecting both protein-protein and protein-DNA interactions, play a crucial role in finely tuning all processes involved in the restoration of genome lesions. Regarding damaged chromatin, PTMs serve in many cases as recruitment platforms for DNA repair mechanisms by facilitating binding sites or regulating interactions between involved proteins. Ubiquitination, the addition of ubiquitin moieties on a target protein, apart from controlling protein availability through degradation, is also involved, together with partner small ubiquitin-like modifier (SUMO), in controlling many pathways involved in DDR by modifying the structure-function relationship and thus interacting with partner molecules. The aim of this book is to cover a broad spectrum of current topics in ubiquitination and to a lesser extent SUMOylation involvement in regulation of DDR and repair in health and disease. This book is intended for pre- and postgraduate students and young scientists in this field. Members of both academic and research institutions, actively involved in the field, have described their current understanding of major mechanisms involved, highlighted key events, described ongoing applications in both developmental diseases and cancer and provided hints for future potential applications.
Microbiology. --- Microbial biology --- Biology --- Microorganisms --- Life Sciences --- Immunology and Microbiology --- Structural Biology --- Proteomics
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Interest in understanding the biological role of carbohydrates has increased significantly over the last 20 years. The use of structural techniques to understand carbohydrate-protein recognition is still a relatively young area, but one that is of emerging importance. The high flexibility of carbohydrates significantly complicates the determination of high quality structures of their complexes with proteins. Specialized techniques are often required to understand the complexity of carbohydrate recognition by proteins. In this Research Topic, we will focus on structural and computational approaches to understanding carbohydrate recognition by proteins involved in immunity and infection. Particular areas of focus include cancer immunotherapeutics, carbohydrate-lectin interactions, glycosylation and glycosyltransferases.
Glycomics. --- infection --- signaling --- molecular modeling --- cancer immunotherapy --- lectins --- molecular recognition --- structural biology --- glycobiology
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cell biology --- nanotechnology --- applied computation and bioinformatics --- structural biology --- structural chemistry --- Biology --- Life sciences --- Chemistry --- Sciences de la vie --- Chimie
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The peripheral membrane proteins transduce the extracellular signaling into the cells. The peripheral membrane proteins include the G protein-coupled receptors, receptor tyrosine kinases, channels and transporters. The signals, which are transduced via the peripheral membrane proteins, activate several pathways including G protein signaling, MAPK signaling, TNF signaling, TGF? signaling, Wnt signaling and Hedgehog signaling. The peripheral membrane proteins transduce the signaling from the extracellular ligands into the cells. This book intends to provide a comprehensive overview of the features and signaling of peripheral membrane proteins, which includes the molecular structure and interaction. The insights into membrane proteins associated with diseases and therapeutics and the effects of drugs and chemicals are also discussed in this book.
Peripheral circulation --- Regulation. --- Regulation of peripheral circulation --- Biological control systems --- Life Sciences --- Immunology and Microbiology --- Structural Biology --- Proteomics
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The human ubiquitin proteasome system (UPS) is comprised of nearly 1000 proteins. Although originally identified as a mechanism of protein destruction, the UPS has numerous additional functions and mediates central signaling events in myriad processes involved in both cellular and organismal health and homeostasis. Numerous pathways within the UPS are implicated in disease, ranging from cancer to neurodegenerative diseases such as Parkinson's. The goal of this book is to deliver a collection of synopses of current areas of UPS research that highlights the importance of understanding the biology of the UPS to identify disease-relevant pathways, and the need to elucidate the molecular machinations within the UPS to develop methods for therapeutic modulation of these pathways.
Central nervous system --- Physiology. --- Nervous system, Central --- Nervous system --- Life Sciences --- Immunology and Microbiology --- Structural Biology --- Proteomics
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This book highlights key findings generated during the past years from the main disciplines that constitute Physical Virology, from theoretical physics and simulations to material sciences and vaccines development to structural biology. Each chapter is written by world-class scientists from these areas and is a comprehensive review of where this field stands, as well as the future of Physical Virology. The diversity in the formal training of these scientists results in solving common problems using very distinct approaches, which can produce surprising findings. The multi- and interdisciplinary nature of this field has created a remarkable community that aims at understanding how viruses work and how they can be used in material sciences, chemistry, and biomedicine. Furthermore, the development of Physical Virology has resulted in technological advances that have shaped other fields; for example, it would be impossible to think about the development of Cryo-EM to solve the structure of complex viruses with atomic resolution without the contribution of scientists that created the field of Physical Virology. In the past decade, there has been a great success in the generation of viral systems that can encapsulate drugs, non-viral genetic material, or nanoparticles, as well as in the chemical and genetical modification of virions. Without any doubt in the immediate future, some of these technologies will jump from the bench to the market, creating a revolution in translational and biomedical sciences. The book provides key perspectives for the field, derived from expert´s opinions.
Virology. --- Biophysics. --- Biomolecules. --- Physical biochemistry. --- Macromolecules. --- Biomechanics. --- Biology --- Genetic engineering. --- Structural Biology. --- Molecular Biophysics. --- Gene Delivery. --- Technique.
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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 thorough understanding 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.
Biomolecules. --- Physical biochemistry. --- Macromolecules. --- Molecular biology. --- Biophysics. --- Proteins. --- Bioinformatics. --- Structural Biology. --- Molecular Biology. --- Molecular Biophysics. --- Protein Biochemistry.
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The current book focuses on Mora de Castilla (Rubus glaucus Benth.). It explores aspects, such as origin, phenology, propagation, floral and fruit morphology, arthropod visitors, pollination mechanisms, propagation methods, chromosome number, fruit development, breeding, morphological diversity, and the impact of climate change. It includes novel data about plant phenology, flowering, insect visitors, seed germination, fruit morphology, and allometric relationships. This work includes an in-depth review of the most recently published information on the topic. Mora de Castilla is an economically important fruit crop from the Andes. It has been crossed with other Rubus species due to its high yield and everbearing habit. Currently, it is an economically important plant. It has been hybridized with other Rubus species producing new and better-quality hybrids This book contains numerous photographs selected by the author to provide the reader with detailed information about the plant´s morphological features and arthropod visitors. .
Botany --- Agriculture. Animal husbandry. Hunting. Fishery --- landbouw --- botanie --- planten --- Botany. --- Agriculture. --- Biomolecules. --- Physical biochemistry. --- Macromolecules. --- Plant Science. --- Structural Biology. --- Science
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The chapters in this book are written by a team of well-reputed international researchers. The objective is to provide advanced and updated information related to protein-protein interactions. I hope the methods, resources and approaches described here will enhance the available knowledge of the reader significantly.
Protein-protein interactions. --- Interactions, Protein-protein --- PPIs (Protein-protein interactions) --- Protein interactions --- Interactomes --- Molecular association --- Life Sciences --- Immunology and Microbiology --- Structural Biology --- Proteomics
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