A litmus test for classifying recognition mechanisms of transiently binding proteins
Journal article, 2022

Partner recognition in protein binding is critical for all biological functions, and yet, delineating its mechanism is challenging, especially when recognition happens within microseconds. We present a theoretical and experimental framework based on straight-forward nuclear magnetic resonance relaxation dispersion measurements to investigate protein binding mechanisms on sub-millisecond timescales, which are beyond the reach of standard rapid-mixing experiments. This framework predicts that conformational selection prevails on ubiquitin’s paradigmatic interaction with an SH3 (Src-homology 3) domain. By contrast, the SH3 domain recognizes ubiquitin in a two-state binding process. Subsequent molecular dynamics simulations and Markov state modeling reveal that the ubiquitin conformation selected for binding exhibits a characteristically extended C-terminus. Our framework is robust and expandable for implementation in other binding scenarios with the potential to show that conformational selection might be the design principle of the hubs in protein interaction networks.
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Published in

Nature Communications

2041-1723 (ISSN) 20411723 (eISSN)

Vol. 13 Issue 1 art. no 3792

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Subject Categories (SSIF 2011)

Biophysics

Structural Biology

Bioinformatics and Systems Biology

Identifiers

DOI

10.1038/s41467-022-31374-5

PubMed

35778416

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Latest update

3/17/2025