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Cell Rep. 2016 Jan 5;14(1):32-42. doi: 10.1016/j.celrep.2015.12.010. Epub 2015 Dec 24.

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

Author information

1
Howard Hughes Medical Institute, Brandeis University, 415 South Street, Waltham, MA 02454; Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454.
2
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
3
Paul Scherrer Institute, 5232 Viligan PSI, Switzerland.
4
Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454. Electronic address: oprian@brandeis.edu.
5
Howard Hughes Medical Institute, Brandeis University, 415 South Street, Waltham, MA 02454; Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454. Electronic address: dkern@brandeis.edu.

Abstract

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.

KEYWORDS:

conformational ensemble; conformational selection; energy landscape; molecular recognition dynamics; protein/protein interaction; recoverin

PMID:
26725117
PMCID:
PMC4706811
DOI:
10.1016/j.celrep.2015.12.010
[Indexed for MEDLINE]
Free PMC Article

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