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The transition state structure for binding between TAZ1 of CBP and the disordered Hif-1 alpha CAD
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Number of Authors: 32018 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 8, article id 7872Article in journal (Refereed) Published
Abstract [en]

Intrinsically disordered proteins (IDPs) are common in eukaryotes. However, relatively few experimental studies have addressed the nature of the rate-limiting transition state for the coupled binding and folding reactions involving IDPs. By using site-directed mutagenesis in combination with kinetics measurements we have here characterized the transition state for binding between the globular TAZ1 domain of CREB binding protein and the intrinsically disordered C-terminal activation domain of Hif-1 alpha (Hif-1 alpha CAD). A total of 17 Hif-1 alpha CAD point-mutations were generated and a F-value binding analysis was carried out. We found that native hydrophobic binding interactions are not formed at the transition state. We also investigated the effect the biologically important Hif-1 alpha CAD Asn-803 hydroxylation has on the binding kinetics, and found that the whole destabilization effect due the hydroxylation is within the dissociation rate constant. Thus, the rate-limiting transition state is disordered-like, with native hydrophobic binding contacts being formed cooperatively after the rate-limiting barrier, which is clearly shown by linear free energy relationships. The same behavior was observed in a previously characterized TAZ1/IDP interaction, which may suggest common features for the rate-limiting transition state for TAZ1/IDP interactions.

Place, publisher, year, edition, pages
2018. Vol. 8, article id 7872
National Category
Biochemistry Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-157742DOI: 10.1038/s41598-018-26213-xISI: 000432441400060PubMedID: 29777197Scopus ID: 2-s2.0-85047190735OAI: oai:DiVA.org:su-157742DiVA, id: diva2:1236304
Available from: 2018-08-01 Created: 2018-08-01 Last updated: 2025-02-20Bibliographically approved
In thesis
1. Biophysical characterization of protein-protein interactions involving intrinsically disordered proteins
Open this publication in new window or tab >>Biophysical characterization of protein-protein interactions involving intrinsically disordered proteins
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Intrinsically disordered proteins and regions (IDPs/Rs) are proteins that do not form stable and well-defined structures in their free states but rather occupy an ensemble of conformations that change over time while still staying functional. They are prevalent in the eukaryotic proteome and are involved in various vital processes in the cell where they often interact with their binding partners through coupled binding and folding reactions. The knowledge on the molecular details of these interactions is still limited as is the role of dynamics and conformational entropy changes. In this thesis binding interactions between IDPs and a folded protein domain have been studied in more detail. The rate-limiting transition states (TS) of binding have been examined using kinetic experiments and protein engineering (F-value analysis), and the picosecond to nanosecond backbone and side-chain dynamics of these interactions have been studied with nuclear magnetic resonance (NMR) spectroscopy. To study these properties the globular TAZ1 domain of the CREB binding protein (CBP) and three of its interaction partners, the disordered transactivation domains of STAT2, HIF-1a and RelA have been selected. At the rate limiting transition states of binding for TAZ1/TAD-STAT2 and TAZ1/CTAD-HIF-1a native hydrophobic binding contacts are largely absent. These interactions are instead formed cooperatively after passing the rate-limiting barrier. The results from the backbone and side-chain dynamic studies show that the internal motions for both binding partners are significantly affected by the interactions. Changes in dynamics upon binding correspond to conformational entropy changes that contribute significantly to the binding thermodynamics, and are in the same order of magnitude as the binding enthalpy. Additionally, the conformational entropy changes for TAZ1 vary when binding to the different IDPs, demonstrating the importance of conformational entropy. In conclusion, this work contributes to the understanding of the nature of binding interactions involving intrinsically disordered proteins.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2021. p. 54
Keywords
Intrinsically disordered proteins, Protein-protein interactions, Disorder-to-order transition, Rate-limiting transition state, Ф-value analysis, NMR relaxation, Side-chain dynamics, Backbone dynamics, Conformational entropy change
National Category
Biophysics
Research subject
Biophysics
Identifiers
urn:nbn:se:su:diva-186770 (URN)978-91-7911-370-4 (ISBN)978-91-7911-371-1 (ISBN)
Public defence
2021-01-29, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2020-12-21 Created: 2020-11-25 Last updated: 2025-02-20Bibliographically approved

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Lindström, IdaDogan, Jakob

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