Allostery, 2012
Methods and Protocols
Methods in Molecular Biology Series, Vol. 796

Despite considerable variability within the scientific community, allosteric regulation can best be defined functionally as how a macromolecule binds one ligand differently when a second ligand is or is not pre-bound to the macromolecule, which constitutes a vital aspect of protein structure/function.  In Allostery: Methods and Protocols, expert researchers in the field provide key techniques to investigate this biological phenomenon.  Focusing on heterotropic systems with some coverage of homotropic systems, this volume covers the monitoring of allosteric function, allosteric conformational changes, and allosteric changes in protein dynamics/sub-population distribution, as well as topics such as macromolecular and ligand engineering of allosteric functions and computational aids in the study of allostery. Written in the highly successful Methods in Molecular Biology? series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory.

Binding Techniques to Study the Allosteric Energy Cycle.- Kinetic Trapping of a Key Hemoglobin Intermediate.- Allosteric Coupling Between Transition Metal Binding Sites in Homooligomeric Metal Sensor Proteins.- Studying the Allosteric Energy Cycle by Isothermal Titration Calorimetry.- Detecting “Silent” Allosteric Coupling.- Using Mutant Cycle Analysis to Elucidate Long-Range Functional Coupling in Allosteric Receptors.- A Review of Methods Used for Identifying Structural Changes in a Large Protein Complex.- Allosteric Mechanisms of G Protein-Coupled Receptor Signaling: A Structural Perspective.- Dynamic Light Scattering to Study Allosteric Regulation.- Dissecting the Linkage Between Transcription Factor Self-Assembly and Site-Specific DNA Binding: The Role of the Analytical Ultracentrifuge.- Fluorescence Correlation Spectroscopy and Allostery: The Case of GroEL.- The Morpheein Model of Allostery: Evaluating Proteins as Potential Morpheeins.- Combining NMR and Molecular Dynamics Studies for Insights into the Allostery of Small GTPase-Protein Interactions.- H/D-Exchange Study of an Allosteric Energy Cycle.- Ensemble Properties of Network Rigidity Reveal Allosteric Mechanisms.- An In Vivo Approach to Isolating Allosteric Pathways Using Hybrid Multimeric Proteins.- Mutations in the GABA_A Receptor that Mimic the Allosteric Ligand, Etomidate.- Allosteric Regulation of Human Liver Pyruvate Kinase by Peptides that Mimic the Phosphorylated/Dephosphorylated N-Terminus.- In Silico Screening Approaches for Lead Generation: Identification of Novel Allosteric Modulators of Human-Erythrocyte Pyruvate Kinase.- Identification of Allosteric-Activating Drug Leads for Human Liver Pyruvate Kinase.- A Critical Evaluation of Correlated Mutation Algorithms and Coevolution Within Allosteric Mechanisms.- The Advantage ofGlobal Fitting of Data Involving Complex Linked Reactions.- Predicting Binding Sites by Analyzing Allosteric Effects.