Journal article
Conformational Dynamics and Cooperativity Drive the Specificity of a Protein-Ligand Interaction
Biophysical journal, Vol.116(12), pp.2314-2330
06/18/2019
DOI: 10.1016/j.bpj.2019.05.008
PMCID: PMC6588728
PMID: 31146922
Abstract
Molecular recognition is critical for the fidelity of signal transduction in biology. Conversely, the disruption of protein-protein interactions can lead to disease. Thus, comprehension of the molecular determinants of specificity is essential for understanding normal biological signaling processes and for the development of precise therapeutics. Although high-resolution structures have provided atomic details of molecular interactions, much less is known about the influence of cooperativity and conformational dynamics. Here, we used the Tiam2 PSD-95/Dlg/ZO-1 (PDZ) domain and a quadruple mutant (QM), engineered by swapping the identity of four residues important for specificity in the Tiam1 PDZ into the Tiam2 PDZ domain, as a model system to investigate the role of cooperativity and dynamics in PDZ ligand specificity. Surprisingly, equilibrium binding experiments found that the ligand specificity of the Tiam2 QM was switched to that of the Tiam1 PDZ. NMR-based studies indicated that Tiam2 QM PDZ, but not other mutants, had extensive microsecond to millisecond motions distributed throughout the entire domain suggesting structural cooperativity between the mutated residues. Thermodynamic analyses revealed energetic cooperativity between residues in distinct specificity subpockets that was dependent upon the identity of the ligand, indicating a context-dependent binding mechanism. Finally, isothermal titration calorimetry experiments showed distinct entropic signatures along the mutational trajectory from the Tiam2 wild-type to the QM PDZ domain. Collectively, our studies provide unique insights into how structure, conformational dynamics, and thermodynamics combine to modulate ligand-binding specificity and have implications for the evolution, regulation, and design of protein-ligand interactions.
Details
- Title: Subtitle
- Conformational Dynamics and Cooperativity Drive the Specificity of a Protein-Ligand Interaction
- Creators
- Xu Liu - University of IowaLisa C. Golden - University of IowaJosue A. Lopez - University of IowaTyson R. Shepherd - University of IowaLiping Yu - University of IowaErnesto J. Fuentes - Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Resource Type
- Journal article
- Publication Details
- Biophysical journal, Vol.116(12), pp.2314-2330
- DOI
- 10.1016/j.bpj.2019.05.008
- PMID
- 31146922
- PMCID
- PMC6588728
- NLM abbreviation
- Biophys J
- ISSN
- 0006-3495
- eISSN
- 1542-0086
- Publisher
- Elsevier
- Number of pages
- 17
- Grant note
- R21AI135305 / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) R21 AI135305; T32 GM008365 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA T32GM008365 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) E155500; 0835261N / American Heart Association
- Language
- English
- Date published
- 06/18/2019
- Academic Unit
- Biochemistry and Molecular Biology; Medicine Administration
- Record Identifier
- 9984288733802771
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