Description
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(TM) series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Allostery: Methods and Protocols aids scientists in continuing to study ligand-induced, through-protein effects on protein function (ligand binding/catalysis), a phenomenon that is well recognized through the history of the life sciences and very poorly understood at the molecular level. Part I: Monitoring Allosteric Function 1. Binding Techniques to Study the Allosteric Energy Cycle James K. Kranz and Jose C. Clemente 2. Kinetic Trapping of a Key Hemoglobin Intermediate Jo M. Holt and Gary K. Ackers 3. Allosteric Coupling Between Transition Metal Binding Sites in Homooligomeric Metal Sensor Proteins Nicholas E. Grossoehme and David P. Giedroc 4. Studying the Allosteric Energy Cycle by Isothermal Titration Calorimetry Marta Martinez-Julvez, Olga Abian, Sonia Vega, Milagros Medina, and Adrian Velazquez-Campoy 5. Detecting “Silent” Allosteric Coupling Harvey F. Fisher 6. Using Mutant Cycle Analysis to Elucidate Long-Range Functional Coupling in Allosteric Receptors Jai A.P. Shanata, Shawnalea J. Frazier, Henry A. Lester, and Dennis A. Dougherty Part II: Monitoring Allosteric Conformational Changes 7. A Review of Methods Used for Identifying Structural Changes in a Large Protein Complex Owen W. Nadeau and Gerald M. Carlson 8. Allosteric Mechanisms of G Protein-Coupled Receptor Signaling: A Structural Perspective Tarjani M. Thaker, Ali I. Kaya, Anita M. Preininger, Heidi E. Hamm, and T.M. Iverson 9. Dynamic Light Scattering to Study Allosteric Regulation Aaron L. Lucius, P. Keith Veronese, and Ryan P. Stafford 10. Dissecting the Linkage Between Transcription Factor Self-Assembly and Site-Specific DNA Binding: The Role of the Analytical Ultracentrifuge Amie D. Moody, James P. Robblee, and David L. Bain 11. Fluorescence Correlation Spectroscopy and Allostery: The Case of GroEL Gabriel A. Frank, Amnon Horovitz, and Gilad Haran 12. The Morpheein Model of Allostery: Evaluating Proteins as Potential Morpheeins Eileen K. Jaffe and Sarah H. Lawrence Part III: Monitoring Allosteric Changes in Protein Dynamics/Sub-Population Distribution 13. Combining NMR and Molecular Dynamics Studies for Insights into the Allostery of Small GTPase-Protein Interactions Liqun Zhang, Sabine Bouguet-Bonnet, and Matthias Buck 14. H/D-Exchange Study of an Allosteric Energy Cycle Dorothy Beckett 15. Ensemble Properties of Network Rigidity Reveal Allosteric Mechanisms Donald J. Jacobs, Dennis R. Livesay, James M. Mottonen, Oleg K. Vorov, Andrei Y. Istomin, and Deeptak Verma Part IV: Macromolecular and Ligand Engineering Allosteric Functions 16. An In Vivo Approach to Isolating Allosteric Pathways Using Hybrid Multimeric Proteins Cuijuan Tie and Gregory D. Reinhart 17. Mutations in the GABAA Receptor that Mimic the Allosteric Ligand, Etomidate Stuart A. Forman and Deirdre Stewart 18. Allosteric Regulation of Human Liver Pyruvate Kinase by Peptides that Mimic the Phosphorylated/Dephosphorylated N-Terminus Charulata B. Prasannan, Qingling Tang, and Aron W. Fenton 19. In Silico Screening Approaches for Lead Generation: Identification of Novel Allosteric Modulators of Human-Erythrocyte Pyruvate Kinase Ashutosh Tripathi and Martin K. Safo 20. Identification of Allosteric-Activating Drug Leads for Human Liver Pyruvate Kinase Aron W. Fenton Part V: Computational Methods/Aids in the Study of Allostery 21. A Critical Evaluation of Correlated Mutation Algorithms and Coevolution Within Allosteric Mechanisms Dennis R. Livesay, Kyle E. Kreth, and Anthony A. Fodor 22. The Advantage of Global Fitting of Data Involving Complex Linked Reactions Petr Herman and J. Ching Lee 23. Predicting Binding Sites by Analyzing Allosteric Effects Dengming Ming and Michael E. Wall
