Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis

• Main Authors: Kalyan S. Chakrabarti, Roman V. Agafonov, Francesco Pontiggia, Renee Otten, Matthew K. Higgins, Gebhard F.X. Schertler, Daniel D. Oprian, Dorothee Kern
• Format: Article
• Language: English
• Published: Elsevier 2016-01-01
• Series: Cell Reports
• Subjects: conformational ensemble; conformational selection; energy landscape; molecular recognition dynamics; protein/protein interaction; recoverin
• Online Access: http://www.sciencedirect.com/science/article/pii/S2211124715014230

Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here, we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsin kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using nuclear magnetic resonance (NMR) spectroscopy, stopped-flow kinetics, and isothermal titration calorimetry, we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Protein dynamics in free recoverin limits the overall rate of binding.