Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Dynamics, Conformational Entropy, and Frustration in Protein-Protein Interactions Involving an Intrinsically Disordered Protein Domain
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Number of Authors: 22018 (English)In: ACS Chemical Biology, ISSN 1554-8929, E-ISSN 1554-8937, Vol. 13, no 5, p. 1218-1227Article in journal (Refereed) Published
Abstract [en]

Intrinsically disordered proteins (IDPs) are abundant in the eukaryotic proteome. However, little is known about the role of subnanosecond dynamics and the conformational entropy that it represents in protein-protein interactions involving IDPs. Using nuclear magnetic resonance side chain and backbone relaxation, stopped-flow kinetics, isothermal titration calorimetry, and computational studies, we have characterized the interaction between the globular TAZ1 domain of the CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2). We show that the TAZ1/TAD-STAT2 complex retains considerable subnanosecond motions, with TAD-STAT2 undergoing only a partial disorder-to-order transition. We report here the first experimental determination of the conformational entropy change for both binding partners in an IDP binding interaction and find that the total change even exceeds in magnitude the binding enthalpy and is comparable to the contribution from the hydrophobic effect, demonstrating its importance in the binding energetics. Furthermore, we show that the conformational entropy change for TAZ1 is also instrumental in maintaining a biologically meaningful binding affinity. Strikingly, a spatial clustering of very high amplitude motions and a cluster of more rigid sites in the complex exist, which through computational studies we found to overlap with regions that experience energetic frustration and are less frustrated, respectively. Thus, the residual dynamics in the bound state could be necessary for faster dissociation, which is important for proteins that interact with multiple binding partners.

Place, publisher, year, edition, pages
2018. Vol. 13, no 5, p. 1218-1227
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-157806DOI: 10.1021/acschembio.7b01105ISI: 000432900600015PubMedID: 29614221OAI: oai:DiVA.org:su-157806DiVA, id: diva2:1235069
Conference
6th Annual Conference of the International Chemical Biology Society (ICBS), China, October 17-20, 2017
Available from: 2018-07-24 Created: 2018-07-24 Last updated: 2022-02-26Bibliographically 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

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMed

Authority records

Lindström, IdaDogan, Jakob

Search in DiVA

By author/editor
Lindström, IdaDogan, Jakob
By organisation
Department of Biochemistry and Biophysics
In the same journal
ACS Chemical Biology
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 36 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf