الصفحة 1
الصفحة 1
New Algorithms for Macromolecular Simulation
Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.
Molecular Chaperones in Health and Disease
Molecular chaperones are involved in a wide variety of essential cellular processes in living cells. A subset of molecular chaperones have been initially described as heat shock proteins protecting cells from stress damage by keeping cellular proteins in a folding competent state and preventing them from irreversible aggregation. Later it became obvious that molecular chaperones are also expressed constitutively in the cell and are involved in complex processes such as protein synthesis, intracellular protein transport, post-translational modification and secretion of proteins as well as receptor signalling. Hence, it is not surprising that molecular chaperones are implicated in the pathogenesis of many relevant diseases and could be regarded as potential pharmacological targets. Starting with the analysis of the mode of action of chaperones at the molecular, cellular and organismic level, this book will then describe specific aspects where modulation of chaperone action could be of pharmacological and therapeutic interest.
Misbehaving Proteins : Protein (Mis)Folding, Aggregation, and Stability
Misfoldedaggregatedproteinoncewasconsideredasinterestingasyesterday’strash—a bothersome by-product of important and productive activities, to be disposed of and forgotten as quickly as possible. Yesterday’s trash has become today’s focus of cons- erable scienti?c interest for at least two reasons: (1) protein aggregates are at the core of a number of chronic degenerative diseases such as Alzheimer’s disease, and (2) - gregation poses signi?cant obstacles to the manufacture of safe, ef?cacious, and stable protein products. As interest in protein misfolding, aggregation, and stability has soared beyond the core group of traditional protein-folding scientists, and as substantial scienti?c progress in understanding and controlling protein misfolding has been achieved, the need to summarize the state of the art became manifest. Although there are many excellent texts and edited collections on protein structure and folding, these volumes tend to relegate protein misfolding and aggregation to a minor role. Review articles and books focused on the biological role of protein aggregates in diseases have been published recently.
Methods in Modern Biophysics
Incorporating recent dramatic advances, this textbook presents a fresh and timely introduction to modern biophysical methods. An array of new, faster and higher-power biophysical methods now enables scientists to examine the mysteries of life at a molecular level. This innovative text surveys and explains the ten key biophysical methods, including those related to biophysical nanotechnology, scanning probe microscopy, X-ray crystallography, ion mobility spectrometry, mass spectrometry, proteomics, and protein folding and structure. Incorporating much information previously unavailable in tutorial form, Nölting employs worked examples and 267 illustrations to fully detail the techniques and their underlying mechanisms.
Heat Shock Proteins and the Brain : Implications for Neurodegenerative Diseases and Neuroprotection
Neurodegenerative disorders such as Alzheimer’s disease, Huntington’s disease, Parkinson’s disease and amyotrophic lateral sclerosis have been termed ‘protein misfolding disorders’ that are char- terized by the neural accumulation of protein aggregates. Manipulation of the cellular stress response involving the induction of heat shock proteins offers a the- peutic strategy to counter conformational changes in neural proteins that trigger pathogenic cascades resulting in neurodegenerative diseases. Heat shock proteins are protein repair agents that provide a line of defense against misfolded, aggregati- prone proteins. Heat Shock Proteins and the Brain: Implications for Neurodegenerative Diseases and Neuroprotection reviews current progress on neural heat shock proteins (HSP) in relation to neurodegenerative diseases (Part I), neuroprotection (Part II), ext- cellular HSP (Part III) and aging and control of life span (Part IV).
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. Introduces basic rules for protein folding, along with the conditions that result in misfolding Presents research that lies in treating the aqueous environment as a continuum rather than a set of individual water molecules (i.e. the classic representation) Provides practical applications for helping the prevention of amyloidosis and improving drug design
Feasibility and Infeasibility in Optimization : Algorithms and Computational Methods
Feasibility and Infeasibility in Optimization is a timely expository book that summarizes the state of the art in both classical and recent algorithms related to feasibility and infeasibility in optimization, with a focus on practical methods. All model forms are covered, including linear, nonlinear, and mixed-integer programs. Connections to related work in constraint programming are shown. Part I of the book addresses algorithms for seeking feasibility quickly, including new methods for the difficult cases of nonlinear and mixed-integer programs. Part II provides algorithms for analyzing infeasibility by isolating minimal infeasible (or maximum feasible) subsets of constraints, or by finding the best repair for the infeasibility. Infeasibility analysis algorithms have arisen primarily over the last two decades, and the book covers these in depth and detail. Part III describes applications in numerous areas outside of direct infeasibility analysis such as finding decision trees for data classification, analyzing protein folding, radiation treatment planning, automated test assembly, etc.
Computer simulations in condensed matter : From materials to chemical biology ; Vol.1
This extensive and comprehensive collection of lectures by world-leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 1 is an in-depth introduction to a vast spectrum of computational techniques for statistical mechanical systems of condensed matter. It will enable the graduate student and both the specialist and nonspecialist researcher to get acquainted with the tools necessary to carry out numerical simulations at an advanced level. Volume 2 published as LNP 704 (ISBN 3-540-35283-X) is a collection of state-of-the-art surveys on numerical experiments carried out for a great number of systems, ranging from materials sciences to chemical biology.
Cell Stress Proteins
This comprehensive volume, written by experts in the field, provides a current understanding of the molecular properties of the heat shock proteins and their roles in health and disease. Cell Stress Proteins includes advances in several aspects of stress protein research, with chapters ranging from basic studies of the role of heat shock proteins in protein folding to reviews examining the breakdown of stress protein regulation during disease. It also provides analysis of the biochemical and molecular properties of heat shock proteins which can be utilized in evaluating their role in human physiology and pathology. Cell Stress Proteins is an ideal book for researchers, clinicians, physicians, and graduate students in the fields of biochemistry, cell biology, microbiology, immunology, and genetics.
Aspects of physical biology : Biological water, protein solutions, transport and replication
The present volume focuses on three main subtopics (biological water, protein solutions as well as transport and replication), presenting for each of the them the on-going debates on recent results. The role of water in biological processes, the mechanisms of protein folding, the phases and cooperative effects in biological solutions, the thermodynamic description of replication, transport and neural activity, all are subjects that are revised in this volume, based on new experiments and new theoretical interpretations.
