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

Kalyan S Chakrabarti, Roman V Agafonov, Francesco Pontiggia, Renee Otten, Matthew K Higgins, Gebhard F X Schertler, Daniel D Oprian, Dorothee Kern

Cell reports 2016 Jan 05

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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. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Citation

Kalyan S Chakrabarti, Roman V Agafonov, Francesco Pontiggia, Renee Otten, Matthew K Higgins, Gebhard F X Schertler, Daniel D Oprian, Dorothee Kern. Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis. Cell reports. 2016 Jan 05;14(1):32-42