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Proteins are essential for all known forms of life and in many lethal diseases protein failure is the cause of the disease. To understand proteins and the processes they are involved in, it is valuable to know their structures as well as their dynamics and interactions. The structures may not be directly inspected because proteins are too small to be visible in a light microscope, which is why indirect methods such as nuclear magnetic resonance (NMR) spectroscopy have to be utilized. This method provides atomic information about the protein and, in contrast to other methods with similar resolution, the measurements are performed in solution resulting in more physiological conditions, enabling analysis of dynamics. Important dynamical processes are the ones on the millisecond timeframe, which may contribute to interactions of proteins and their catalysis of chemical reactions, both of significant value for the function of the proteins. To better understand proteins, not only do we need to study them, but also develop the methods we are using. This thesis presents four papers about improved NMR techniques as well as a fifth where the kinase domain of ephrinB receptor 2 (EphB2) has been studied regarding the importance of millisecond dynamics and interactions for the activation process. The first paper presents the software COMPASS, which combines statistics and the calculation power of a computer with the flexibility and experience of the user to facilitate and speed up the process of assigning NMR signals to the atoms in the protein. The computer program PINT has been developed for easier and faster evaluation of NMR experiments, such as those that evaluate protein dynamics. It is especially helpful for NMR signals that are difficult to distinguish, so called overlapped peaks, and the soft- ware also converts the detected signals to the indirectly measured physical quantities, such as relaxation rate constants, principal for dynamics. Next are two new versions of the Carr-Purcell-Maiboom-Gill (CPMG) dispersion pulse sequences, designed to measure millisecond dynamics in a way so that the signals are more separated than in standard experiments, to reduce problems with overlaps. To speed up the collection time of the data set, a subset is collected and the entire data set is then reconstructed, by multi-dimensional decomposition co-processing. Described in the thesis is also a way to produce suitably labeled proteins, to detect millisecond dynamics at C? positions in proteins, using the CPMG dispersion relaxation experiment at lower protein concentrations. Lastly, the kinase domain of EphB2 is shown to be more dynamic on the millisecond time scale as well as more prone to interact with itself in the active form than in the inactive one. This is important for the receptor function of the protein, when and how it mediates signals. To conclude, this work has extended the possibilities to study protein dynamics by NMR spectroscopy and contributed to increased understanding of the activation process of EphB2 and its signaling mechanism.
Receptor tyrosine kinases are cell-surface receptors that respond to numerous hormones and growth factors, including insulin, insulin-like growth factors, epidermal growth factor, and nerve growth factor. They activate highly conserved intracellular signaling pathways that regulate cell proliferation, differentiation, and metabolism, playing essential roles in developing and adult animals. This book examines the nature of these receptors and their ligands, the molecular mechanisms that they regulate within cells, and the roles of the receptors in normal physiology and control of embryogenesis. It also discusses how dysfunction of these mechanisms can contribute to cancer and other diseases.
Myofibrillogenesis has been studied extensively over the last 100 years. Until recently, we have not had a comprehensive understanding of this fundamental process. The emergence of new technologies in molecular and cellular biology, combined with classical embryology, have started to unravel some of the complexities of myofibril assembly in striated muscles. In striated muscles, the contractile proteins are arranged in a highly ordered three dimensional lattice known as the sarcomere. The assembly of a myofibril involves the precise ordering of several proteins into a linear array of sarcomeres. Multiple isoforms in many of these proteins further complicate the process, making it difficult to define the precise role of each component. This volume has been compiled as a comprehensive reference on myofibrillogenesis. In addition, the book includes reviews on myofibrillar disarray under various pathological conditions, such as familial hypertrophic cardiomyopathy (FHC), and incorporates a section on the conduction system in the heart. Much of the information in this volume has not been described elsewhere. Presented in a manner to be of value to students and teachers alike, "Myofibrillogenesis" will be an invaluable reference source for all in the fields of muscle biology and heart development.
Receptor Tyrosine Kinase: Structure, Functions and Role in Human Disease, for the first time, systematically covers the shared structural and functional features of the RTK family. Receptor Tyrosine Kinases (RTKs) play critical roles in embryogenesis, normal physiology and several diseases. And over the last decade they have become the Number 1 targets of cancer drugs. To be able to conduct fundamental research or to attempt to develop pharmacological agents able to enhance or intercept them, it is essential first to understand the evolutionary origin of the 58 RTKs and their roles in invertebrates and in humans, as well as downstream signaling pathways. The assembly of chapters is written by experts and underscores commonalities between and among the RTKs. It is an ideal companion volume to The Receptor Tyrosine Kinase: Families and Subfamilies, which proceeds, family by family through all of the specific subfamilies of RTKs, along with their unique landmarks.
This book devotes a chapter to each RTK family and the multiple receptors within each family, thoroughly covering all of the RTKs. The chapters all follow the same structure, presenting this essential information in an accessible and user-friendly format. Each chapter covers one specific family of receptors and begins with a general introduction to that family and a comprehensive discussion of that receptor’s family in development and human disease. Following are in-depth analyses of each family’s receptors with discussions on the gene, protein, ligands, activation, and signaling pathways along with discussion of receptor processing and signal attenuation. Further, cross talk with other receptors systems, post-translational modification and specific unique characteristics to each RTK are discussed. Because it isolates and explains each family, this book is an essential companion volume to Receptor Tyrosine Kinases: Structure, Functions and Role in Human Disease, by the same authors, which talks about RTKs more generally and without the family-by-family detail.
This volume details the current understanding of roles and regulation on histidine phosphorylation, describing methods for the characterization of protein phosphorylation on histidine. Chapters guide readers through in vitro systems, cell-based systems, comprehensive background review articles on histidine kinases and phosphatases. 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, Histidine Phosphorylation: Methods and Protocols aims to ensure successful results in the further study of this rapidly growing field.
In recent years, there has been a major expansion of high pressure research providing unique information about systems of interest to a wide range of scientific disciplines. Since nuclear magnetic resonance has been applied to a wide spec trum of problems in chemistry, physics and biochemistry, it is not surprising to find that high pressure NMR techniques have also had many applications in these fields of science. Clearly, the high information content of NMR experiments combined with high pressure provides a powerful tool in modern chem istry. It is the aim of this monograph, in the series on NMR Basic Principles and Progress, to illustrate the wide range of prob lems which can be successfully studied by high pressure NMR. Indeed, the various contributions in this volume discuss studies of interest to physics, chemical physics, biochemistry, and chemical reaction kinetics. In many different ways, this monograph demonstrates the power of modern experimental and theoretical techniques to investigate very complex systems. The first contribution, by D. Brinkman, deals with NMR and NQR studies of superionic conductors and high-Tc supercon ductors at high pressure. Pressure effects on phase transitions, detection of new phases, and pressure effects on diffusion and spin-lattice relaxation, represent a few of the topics discussed in this contribution of particular interest to solid state physics.
Increasing evidence identifies the possibility of restoring function to the damaged brain via exogenous therapies. One major target for these advances is stroke, where most patients can be left with significant disability. Treatments have the potential to improve the victim's quality of life significantly and reduce the time and expense of rehabilitation. Brain Repair After Stroke reviews the biology of spontaneous brain repair after stroke in animal models and in humans. Detailed chapters cover the many forms of therapy being explored to promote brain repair and consider clinical trial issues in this context. This book provides a summary of the neurobiology of innate and treatment-induced repair mechanisms after hypoxia and reviews the state of the art for human therapeutics in relation to promoting behavioral recovery after stroke. Essential reading for stroke physicians, neurologists, rehabilitation physicians and neuropsychologists.
Kinase drug discovery remains an area of significant interest across academia and in the pharmaceutical industry. There are now around 13 FDA approved small molecule drugs which target kinases and many more compounds in various stages of clinical development. Although there have been a number of reviews/publications on kinase research, this book fills a gap in the literature by considering the current and future opportunities and challenges in targeting this important family of enzymes. The book is forward-looking and identifies a number of hot topics and key areas for kinase drug discovery over the coming years. It includes contributions from highly respected authors with a combined experience in the industry of well over 200 years, which has resulted in a book of great interest to the kinase field and across drug discovery more generally. Readers will gain a real insight into the huge challenges and opportunities which this target class has presented drug discovery scientists. The many chapters cover a wide breadth of topics, are well written and include high quality colour and black and white images. Topics covered include an outline of how medicinal chemistry has been able to specifically exploit this unique target class, along with reflections on the mechanisms of kinases inhibitors. Also covered is resistance to kinase inhibitors caused by amino acid mutations, case studies of kinase programs and reviews areas beyond protein kinases and beyond the human kinome. Also described are modern approaches to finding kinase leads and the book finishes with a reflection of how kinase drug discovery may progress over the coming years.