Linkage Thermodynamics Of Macromolecular Interactions

This volume commemorates the 50th anniversary of the appearance in Volume 4 in 1948 of Dr. Jeffries Wyman's famous paper in which he "laid down" the foundations of linkage thermodynamics. Experts in this area contribute articles on the state-of-the-art of this important field and on new developments of the original theory. Among the topics covered in this volume are electrostatic contributions to molecular free energies in solution; site-specific analysis of mutational effects in proteins; allosteric transitions of the acetylcholine receptor; and deciphering the molecular code of hemoglobin allostery.

Ligand-macromolecule interactions are of fundamental importance in the control of biological processes. This book applies the principles of linkage thermodynamics to polyfunctional macromolecular systems under equilibrium conditions, and describes the binding, linkage, and feedback phenomena that lead to control of complex metabolic processes. The first chapter sets out the different processes (conformational changes, changes in state of aggregation, phase changes) involving biological macromolecules which are affected by chemical variables (such as ligands) or physical variables (such as temperature and pressure). The general effects of ligands on micromolecular conformations and interactions are illustrated with specific examples from the respiratory proteins, electron-transport proteins, and nucleic acid binding proteins. Subsequent chapters develop these themes, and describe in detail how the mathematics of regulation and control can be applied to macromolecules in biological system.

This volume successfully and clearly examines how biophysical approaches can be used to study complex systems of reversibly interacting proteins. It deals with the methodology behind the research and shows how to synergistically incorporate several methodologies for use. Each chapter treats and introduces the reader to different biological systems, includes a brief summary of the physical principles, and mentions practical requirements.

This compact, graduate-level text focuses on a key area of biophysical chemistry. Introduction to Macromolecular Binding Equilibria first describes the features of binding sites for small molecules and then presents a discussion of the formulation of binding isotherms for simple mathematical models. The book addresses special problems in describing isotherms for linear polymers and examines the complications of binding cooperativity and thermodynamic linkage interactions among multiple ligands. It highlights important aspects of experimental designs, key aspects of ligand binding to planar arrays of sites, and methods for model-free analysis data used to reveal the binding isotherm.

Ligand binding by macromolecules represents a core event of broad relevance to a range of systems, including catalytic systems alongside noncatalytic systems such as nucleic acid binding by transcription factors or extracellular ligand binding by proteins involved in signaling pathways. The scope of this primer is constrained to introduce only foundational models without significant discussion of more advanced topics such as allosteric or linkage effects. Linkage occurs when the binding of a ligand is influenced by the binding of another molecule of the same ligand (homotropic linkage), the binding of a different ligand (heterotropic linkage), physical variables such as temperature or pressure (physical linkage), or changes in macromolecular assembly state (polysteric linkage). Taking this into account, the foundational themes presented in this primer can be used to describe any macromolecule–ligand interaction either by direct use of the models and techniques described here or by applying them to develop more advanced models to explain additional complexities such as those allosteric or linkage effects just mentioned. The target audience of this primer is the senior undergraduate or junior graduate student who lacks a foundation in ligand-binding thermodynamics. As such, we have focused primarily on foundational thermodynamic treatments and presented only general discussions of relevant experimental designs. Readers of this primer will learn how to build a working understanding of common factors that promote energetic favorability for ligand binding; develop a functional toolbox to understand ligand binding from the perspective of collecting, plotting, and interpreting ligand-binding data; enhance proficiency in deriving thermodynamic mechanisms for ligand binding; and become comfortable in interpreting binding data reported in the literature and independently expanding knowledge beyond the scope introduced in this primer.

Reductionism as a scientific methodology has been extraordinarily successful in biology. However, recent developments in molecular biology have shown that reductionism is seriously inadequate in dealing with the mind-boggling complexity of integrated biological systems. This title presents an appropriate balance between science and philosophy and covers traditional philosophical treatments of reductionism as well as the benefits and shortcomings of reductionism in particular areas of science. Discussing the issue of reductionism in the practice of medicine it takes into account the holistic and integrative aspects that require the context of the patient in his biological and psychological entirety. The emerging picture is that what first seems like hopeless disagreements turn out to be differences in emphasis. Although genes play an important role in biology, the focus on genetics and genomics has often been misleading. The consensus view leads to pluralism: both reductionst methods and a more integrative approach to biological complexity are required, depending on the questions that are asked. * An even balance of contributions from scientists and philosophers of science - representing a unique interchange between both communities interested in reductionism

A reissue of a classic book -- corrected, edited, typeset, redrawn, and indexed for the Biological Physics Series. Intended for undergraduate courses in biophysics, biological physics, physiology, medical physics, and biomedical engineering, this is an introduction to statistical physics with examples and problems from the medical and biological sciences. Topics include the elements of the theory of probability, Poisson statistics, thermal equilibrium, entropy and free energy, and the second law of thermodynamics. It can be used as a supplement to standard introductory physics courses, and as a text for medical schools, medical physics courses, and biology departments. The three volumes combined present all the major topics in physics. These books are being reissued in response to frequent requests to satisfy the growing need among students and practitioners in the medical and biological sciences with a working knowledge of the physical sciences. The books are also in demand in physics departments either as supplements to traditional intro texts or as a main text for those departments offering courses with biological or medical physics orientation.

Energetics of Biological Macromolecules, Part E focuses on methods related to allosteric enzymes and receptors, including fluorescent proves, spectroscopic methods and quantitative analysis as well as on cooperativity in protein folding. NMR and mass spectrometry methods are discussed. Allosteric Enzymes and Receptors Cooperativity in Protein Folding and Assembly