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A single-molecule dissection of ligand binding to a protein with intrinsic dynamics

Abstract

Protein dynamics have been suggested to have a crucial role in biomolecular recognition, but the precise molecular mechanisms remain unclear. Herein, we performed single-molecule fluorescence resonance energy transfer measurements for wild-type maltose-binding protein (MBP) and its variants to demonstrate the interplay of conformational dynamics and molecular recognition. Kinetic analysis provided direct evidence that MBP recognizes a ligand through an 'induced-fit' mechanism, not through the generally proposed selection mechanism for proteins with conformational dynamics such as MBP. Our results indicated that the mere presence of intrinsic dynamics is insufficient for a 'selection' mechanism. An energetic analysis of ligand binding implicated the critical role of conformational dynamics in facilitating a structural change that occurs upon ligand binding.

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Figure 1: Molecular recognition processes for induced-fit and conformational selection mechanisms.
Figure 2: Experimental design for analyzing the conformational dynamics of MBP.
Figure 3: Analysis of intrinsic dynamics of MBPs through smFRET.
Figure 4: Kinetic analysis of conformational dynamics for MBPs in the presence of a ligand.
Figure 5: Simultaneous analysis of Cy7-maltose binding and conformational dynamics of the double mutant through three-color smFRET.

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Acknowledgements

This work was supported by the Pioneer Research Program for Converging Technology (2008-2000218), Advanced Biomass R&D Center (2011-0031363), the Intelligent Synthetic Biology Center (2011-0031950) and the Brain Korea 21 program of the Ministry of Education, Science and Technology (H.-S.K.) and Creative Research Initiatives (2009-0081562) and the World-Class University program of the National Research Foundation of Korea (S.H.). We thank S. Mowbray and D.D. Boehr for helpful discussions.

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E.K. and J.M.C. prepared and characterized the MBP variants. E.K. and S.L. designed, performed and analyzed the single-molecule experiments. A.J and H.-S.L prepared and characterized the Cy7-maltose. E.K., S.L., S.H. and H.-S.K. interpreted the data and wrote the manuscript.

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Correspondence to Sungchul Hohng or Hak-Sung Kim.

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Kim, E., Lee, S., Jeon, A. et al. A single-molecule dissection of ligand binding to a protein with intrinsic dynamics. Nat Chem Biol 9, 313–318 (2013). https://doi.org/10.1038/nchembio.1213

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