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Understanding the functions and properties of molecules in living systems requires a detailed knowledge of their three-dimensional structures and the conformational variability that allows them to adopt multiple functional forms. Interpreting biological systems in the language of three-dimensional structures is of fundamental importance and innumerable research groups around the world are working in this area. This book is a compilation of articles describing attempts at understanding the intricacies of biological systems through the structures of and interactions between their constituent molecules.
This volume is primarily a compilation of contributed articles representing the impact and application of Ramachandran's work on conformation analysis of biopolymers, as well as recent advances in macromolecular structural biology, involving diverse experimental and computational approaches. This volume is being published to coincide with a conference on "Biomolecular Forms and Functions: A celebration of 50 years of the Ramachandran Map" being held at the Indian Institute of Science, Bangalore, in January 2013.
Understanding the functions and properties of molecules in living systems requires a detailed knowledge of their three-dimensional structures and the conformational variability that allows them to adopt multiple functional forms. Interpreting biological systems in the language of three-dimensional structures is of fundamental importance and innumerable research groups around the world are working in this area. This book is a compilation of articles describing attempts at understanding the intricacies of biological systems through the structures of and interactions between their constituent molecules.
Alternative techniques and tools for analyzing biomolecular networks With the recent rapid advances in molecular biology, high-throughput experimental methods have resulted in enormous amounts of data that can be used to study biomolecular networks in living organisms. With this development has come recognition of the fact that a complicated living organism cannot be fully understood by merely analyzing individual components. Rather, it is the interactions of components or biomolecular networks that are ultimately responsible for an organism's form and function. This book addresses the important need for a new set of computational tools to reveal essential biological mechanisms from a systems biology approach. Readers will get comprehensive coverage of analyzing biomolecular networks in cellular systems based on available experimental data with an emphasis on the aspects of network, system, integration, and engineering. Each topic is treated in depth with specific biological problems and novel computational methods: GENE NETWORKS—Transcriptional regulation; reconstruction of gene regulatory networks; and inference of transcriptional regulatory networks PROTEIN INTERACTION NETWORKS—Prediction of protein-protein interactions; topological structure of biomolecular networks; alignment of biomolecular networks; and network-based prediction of protein function METABOLIC NETWORKS AND SIGNALING NETWORKS—Analysis, reconstruction, and applications of metabolic networks; modeling and inference of signaling networks; and other topics and new trends In addition to theoretical results and methods, many computational software tools are referenced and available from the authors' Web sites. Biomolecular Networks is an indispensable reference for researchers and graduate students in bioinformatics, computational biology, systems biology, computer science, and applied mathematics.
Biomolecular Structure and Function covers the proceedings of the 1977 ?Cellular Function and Molecular Structure: Biophysical Approaches to Biological Problems? symposium. It summarizes the application of several biophysical techniques to molecular research in biology. This book starts by describing the use of deuterium-labeled lipids, as monitors of the degree of organization of membrane lipids. It also describes the use of carbon-13-labeled lipids, as indicators of molecular mobility. It explains the lipid-protein interactions involving two integral membrane proteins, mitochondrial cytochrome oxidase and calcium-dependent ATPase of muscle sarcoplasmic reticulum. The book goes on to present NMR studies on the organization and conformation of phospholipids, chloroplast membranes, and erythrocyte membranes. It also presents the ESR study of spectrin-phospholipid associations. It discusses the use of fluorescence probes, electrokinetics, neutron diffraction and ion theory studies of phospholipid-protein association, hormone disease, and senescence effects on prokaryotic and eukaryotic cells. Moreover, this book presents the experiments and phosphorus-31 NMR methodology to simultaneously monitor the intracellular pH and phosphate metabolism in a beating heart, functioning kidney, or an intact living microorganism. This book then describes physical probing of intracellular fluidity and structural changes attending tissue or cell cycles. It also relates relatively narrow lines in the hydrogen-1 NMR spectrum of the extremely viscous complex of the muscle protein troponin and highly polymerized tropomyosin. Structure-function studies of fibrous proteins, such as collagen, actin, and myosin, and active site analysis of enzymes are also presented. Finally, a wide variety of methodologies and technologies is exemplified. This includes proton, carbon, fluorine, phosphorus, and lithium NMR spectroscopy; spin labeling and EPR spectroscopy; chemical studies; light scattering and fluorescence; and electron microscopy.
Biomolecular Structure and Dynamics describes recent fundamental advances in the experimental and theoretical study of molecular dynamics and stochastic dynamic simulations, X-ray crystallography and NMR of biomolecules, the structure of proteins and its prediction, time resolved Fourier transform IR spectroscopy of biomolecules, the computation of free energy, applications of vibrational CD of nucleic acids, and solid state NMR. Further presentations include recent advances in UV resonance Raman spectroscopy of biomolecules, semiempirical MO methods, empirical force fields, quantitative studies of the structure of proteins in water by Fourier transform IR, and density functional theory. Metal-ligand interactions, DFT treatment of organometallic and biological systems, and simulation vs. X-ray and far IR experiments are also discussed in some detail. The book provides a broad perspective of the current theoretical aspects and recent experimental findings in the field of biomolecular dynamics, revealing future research trends, especially in areas where theoreticians and experimentalists could fruitfully collaborate.
This book provides an accessible introduction to the principles and tools for modeling, analyzing, and synthesizing biomolecular systems. It begins with modeling tools such as reaction-rate equations, reduced-order models, stochastic models, and specific models of important core processes. It then describes in detail the control and dynamical systems tools used to analyze these models. These include tools for analyzing stability of equilibria, limit cycles, robustness, and parameter uncertainty. Modeling and analysis techniques are then applied to design examples from both natural systems and synthetic biomolecular circuits. In addition, this comprehensive book addresses the problem of modular composition of synthetic circuits, the tools for analyzing the extent of modularity, and the design techniques for ensuring modular behavior. It also looks at design trade-offs, focusing on perturbations due to noise and competition for shared cellular resources. Featuring numerous exercises and illustrations throughout, Biomolecular Feedback Systems is the ideal textbook for advanced undergraduates and graduate students. For researchers, it can also serve as a self-contained reference on the feedback control techniques that can be applied to biomolecular systems. Provides a user-friendly introduction to essential concepts, tools, and applications Covers the most commonly used modeling methods Addresses the modular design problem for biomolecular systems Uses design examples from both natural systems and synthetic circuits Solutions manual (available only to professors at press.princeton.edu) An online illustration package is available to professors at press.princeton.edu
A collection of articles looking at modern structural biology, summarizing the applications of physical methods - such as x-ray diffraction, high resolution nuclear magnetic resonance and molecular dynamics - to the study of protein structure and dynamics. There is a review of contemporary thoughts within the field, looking at the mechanisms of alloateric transitions and allosteric control, the transmission of information within protein structures and the role of dynamics in determining the specificity of protein - ligand interactions. There is also a look at future innovations.
This is a collection of papers presented and discussed at the first EBSA workshop held at Saltsj6baden outside stockholm in Sweden, July 6-10, 1986. The common theme of these papers is dynamics of biomolecules, and how the dynamics depends on the molecular structure and organi zation, and connects to and determines the biological function. This is a rapidly expanding field of research which combines many different aspects of molecular bio physics. Much material is new and presented for the first time. Even if the work so far has been of the kind that is usually called basic research, practical applications are clearly indicated in some articles, and are waiting around the corner in several other cases. At the workshop only one third of the time was used for the formal presentations and two thirds for discussion. To this should also be added discussions during the poster sessions. During these lively and unrecorded discussions fresh viewpoints emerged and new ideas were created. Ad mittedly, our knowledge at present is only fragmentary but when pieces of the puzzle are brought together at a workshop or in a publication of this kind more extended and sometimes unexpected contours and shapes become vi sible. It is our hope that this rapid publication of camera-ready manuscripts will transfer some of the spi rit at the workshop to the reader, and in his or her institute or laboratory initiate further discussions, bring forward more ideas and start new experimental ap roaches.