Allostery: Methods and Protocols

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: Computation