Cooperative Interactions in Proteins

Johns Hopkins University, Baltimore MD

Investigators

Abstract

The long-range objective of this research is to develop a fundamental description of protein interactions and the mechanisms by which these interactions elicit long-range cooperative effects existing at the core of signaling processes. The goal of this project is to study the interactions of the HIV protein Nef with Lck and Fyn SH3 domains. The following issues will be addressed: 1) The coupling of binding affinity to long range cooperative effects. The proline-rich Nef peptide, the conserved core of Nef, and full length Nef, all bind to SH3 with similar binding affinity but different thermodynamics (different enthalpy/entropy balance; 2) The structural stabilization of Nef by inter-domain interactions; 3) The coupling of binding and inter-domain interactions. These studies will involve a combination of approaches such as experimental thermodynamics (isothermal titration calorimetry and differential scanning calorimetry), hydrogen/deuterium exchange studies, statistical thermodynamic analysis and structure-based thermodynamic computations. The identification and separation of interactions that contribute to binding affinity and cooperative effects from those contributing to binding affinity only, will permit the design of ligands that elicit variable cooperative effects and are able to better modulate protein function. Cells are not bags containing different biological macromolecules performing their function in a random and chaotic fashion. On the contrary, biological macromolecules are tightly regulated by an intricate net of interactions. Different macromolecules communicate with each other through interactions among themselves or with small molecules. These interactions provide the foundation to all the regulatory processes found within living organisms. The long-range objective of this project is to develop a fundamental description of protein interactions and the mechanisms by which these interactions elicit the responses existing at the core of signaling processes.