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

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

doi:10.1016/j.celrep.2015.12.010

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

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 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. Lastly, protein dynamics in free recoverin limits the overall rate of binding.

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

Publication Date:: Fri Jan 01 00:00:00 EST 2016

Research Org.:: Brandeis Univ., Waltham, MA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1394844

Alternate Identifier(s):: OSTI ID: 1239247

Grant/Contract Number:: FG02-05ER15699

Resource Type:: Journal Article: Published Article

Journal Name:: Cell Reports

Additional Journal Information:: Journal Name: Cell Reports Journal Volume: 14 Journal Issue: 1; Journal ID: ISSN 2211-1247

Publisher:: Elsevier

Country of Publication:: Netherlands

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; conformational selection; molecular recognition dynamics; protein/protein interaction; conformational ensemble; energy landscape; recoverin

Citation Formats


                    Chakrabarti, Kalyan S., Agafonov, Roman V., Pontiggia, Francesco, Otten, Renee, Higgins, Matthew K., Schertler, Gebhard F. X., Oprian, Daniel D., and Kern, Dorothee. Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis.  Netherlands: N. p., 2016. 
        Web.  doi:10.1016/j.celrep.2015.12.010.

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                    Chakrabarti, Kalyan S., Agafonov, Roman V., Pontiggia, Francesco, Otten, Renee, Higgins, Matthew K., Schertler, Gebhard F. X., Oprian, Daniel D., & Kern, Dorothee. Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis.  Netherlands.  https://doi.org/10.1016/j.celrep.2015.12.010

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                    Chakrabarti, Kalyan S., Agafonov, Roman V., Pontiggia, Francesco, Otten, Renee, Higgins, Matthew K., Schertler, Gebhard F. X., Oprian, Daniel D., and Kern, Dorothee. 2016.  
        "Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis".  Netherlands.  https://doi.org/10.1016/j.celrep.2015.12.010.

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@article{osti_1394844,

  title        = {Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis},

  author       = {Chakrabarti, Kalyan S. and Agafonov, Roman V. and Pontiggia, Francesco and Otten, Renee and Higgins, Matthew K. and Schertler, Gebhard F. X. and Oprian, Daniel D. and Kern, Dorothee},

  abstractNote = {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 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. Lastly, protein dynamics in free recoverin limits the overall rate of binding.},

  doi          = {10.1016/j.celrep.2015.12.010},

  url          = {https://www.osti.gov/biblio/1394844},
  journal      = {Cell Reports},

  issn         = {2211-1247},

  number       = 1,

  volume       = 14,

  place        = {Netherlands},

  year         = {Fri Jan 01 00:00:00 EST 2016},

  month        = {Fri Jan 01 00:00:00 EST 2016}

}

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

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