A Designed Conformational Shift To Control Protein Binding Specificity
Open accessAbstract
In a conformational selection scenario, manipulating the populations of binding‐competent states should be expected to affect protein binding. We demonstrate how in silico designed point mutations within the core of ubiquitin, remote from the binding interface, change the binding specificity by shifting the conformational equilibrium of the ground‐state ensemble between open and closed substates that have a similar population in the wild‐type protein. Binding affinities determined by NMR titration experiments agree with the predictions, thereby showing that, indeed, a shift in the conformational equilibrium enables us to alter ubiquitin’s binding specificity and hence its function. Thus, we present a novel route towards designing specific binding by a conformational shift through exploiting the fact that conformational selection depends on the concentration of binding‐competent substates.
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Point mutations in the ubiquitin core change binding specificity allosterically by shifting the ground-state ensemble between open and closed substates that have similar populations in the wild-type protein.
“Antibody evolution and conformational changes are similar to point mutations within the ubiquitin core, which changes the binding specificity allosterically by shifting the conformational equilibrium of the ground-state ensemble between open and closed substates that have similar populations in the wild-type protein.521”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [521]
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- Authors
- Michielssens, S., Peters, J. H., Ban, D., Pratihar, S., Seeliger, D., Sharma, M., Giller, K., Sabo, T. M., Becker, S., Lee, D., Griesinger, C., & de Groot, B. L.
- Affiliations
- Max Planck Institute for Biophysical Chemistry (DE)
- ORCID
- Venue
- Angewandte Chemie International Edition
- Publisher
- Wiley
- Published
- 2014-08-12
- Volume
- 53
- Issue
- 39
- Pages
- 10367-10371
- ISSN
- 1433-7851 (ISSN-L)
- 1521-3773
- PMC
- PMC4497613
- OpenAlex
- W2159013987
- Cited by
- 54
- References
- 21
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 1 · 2023: 2 · 2022: 3 · 2021: 3 · 2020: 6 · 2019: 5 · 2018: 3 · 2017: 7 · 2016: 11 · 2015: 6 · 2014: 1
- FWCI
- 3.42
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Angewandte Chemie International Edition (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DORA PSI (Paul Scherrer Institute) (submittedVersion, other-oa)
- Max Planck Digital Library (submittedVersion, other-oa)
- GRO (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- Fonds Wetenschappelijk Onderzoek
- KU Leuven
- Max-Planck-Gesellschaft (233227)
- Vlaamse regering
- Gauss Centre for Supercomputing
- Leibniz-Gemeinschaft
- Leibniz-Rechenzentrum
- FP7 Ideas: European Research Council (233227)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Keywords
- conformational selection, protein binding specificity, ubiquitin, point mutations, conformational equilibrium, protein design, NMR titration, binding affinity, protein-protein interaction
- MeSH terms
- Protein Binding, Thermodynamics, Point Mutation, Nuclear Magnetic Resonance, Biomolecular, Ubiquitin, Molecular Dynamics Simulation
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