Mechanism In Protein Chemistry

This book examines the chemical methods used to study the mechanisms of enzymatically catalyzed reactions with an emphasis on the crystallographic molecular models of active sites. The book traces the development of enzymatic mechanisms from physical organic studies of nonenzymatic catalysis through detailed examination of the specific interactions between catalytic amino acids and intermediate analogues in crystallographic molecular models. The strategies of enzymatic catalysis, such as coenzymatic assistance, approximation, strain, the use of general acid-bases, the involvement of intermediates, and conformational control, are the central topics around which the book is organized.

Includes four new chapters which focus on the repercussions of protein engineering for protein folding and catalysis, this new edition is a more general guide to mechanism in protein science.

The three-dimensional structure of proteins -- Chemical catalysis -- The basic equations of enzyme kinetics -- Measurement and magnitude of individual rate constants -- The pH dependence of enzyme catalysis -- Practical methods for kinetics and equilibria -- Detection of intermediates in enzymatic reactions -- Stereochemistry of enzymatic reactions -- Active-site-directed and enzyme-activated irreversible inhibitors : "affinity labels" and "suicide inhibitors" -- Conformational change, allosteric regulation, motors, and work -- Forces between molecules, and binding energies -- Enzyme-substrate complementarity and the use of binding energy in catalysis -- Specificity and editing mechanisms -- Recombinant DNA technology -- Protein engineering -- Case studies of enzyme structure and mechanism -- Protein stability -- Kinetics of protein folding -- Folding pathways and energy landscapes.

This volume of Advances in Protein Chemistry is devoted to protein folding mechanisms. Some of the topics covered include: autonomous protein folding units, barriers in protein folding reactions, the role of molten globule state in protein folding, comparisons of equilibrium and kinetic approaches for determining protein folding mechanisms, the relationship between sequence and structure in elementary folding units, and the energy landscape theory of protein folding.

The second edition of Structure in Protein Chemistry showcases the latest developments and innovations in the field of protein structure analysis and prediction. The book begins by explaining how proteins are purified and describes methods for elucidating their sequences of amino acids and defining their posttranslational modifications. Comprehensive explanations of crystallography and of noncovalent forces-ionic interactions, hydrogen bonding, and the hydrophobic effect-act as a prelude to an exhaustive description of the atomic details of the structures of proteins. The resulting understanding of protein molecular structure forms the basis for discussions of the evolution of proteins, the symmetry of the oligomeric associations that produce them, and the chemical, mathematical, and physical basis of the techniques used to study their structures. The latter include image reconstruction, nuclear magnetic resonance spectroscopy, proton exchange, optical spectroscopy, electrophoresis, covalent cross-linking, chemical modification, immunochemistry, hydrodynamics, and the scattering of light, X-radiation, and neutrons. These procedures are applied to study the folding of polypeptides and the assembly of oligomers. Biological membranes and their proteins are also discussed. Structure in Protein Chemistry, Second Edition, bridges the gap between introductory biophysical chemistry courses and research literature. It serves as a comprehensive textbook for advanced undergraduates and graduate students in biochemistry, biophysics, and structural and molecular biology. Professionals engaged in chemical, biochemical, and molecular biological research will find it a useful reference.

This volume in the Advances in Protein Chemistry series features cutting-edge articles on topics in protein chemistry. This volume includes chapters on the structural basis of effector regulation and signal termination in heterotrimeric G?n?nproteins; How do receptors activate G proteins; Some mechanistic insights into GPCR activation from detergent solubilized ternary complexes on beads; Activation of G protein coupled receptors; Kinetic analysis of g-protein-coupled receptor signaling using fluorescence resonance energy transfer in living cells; Regulation of Rho Guanine Nucleotide Exchange Factors (RhoGEFs) by G proteins.