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SURFS and AlphaFold Reveal Ribosome Footprint Shift Caused by EF-Tu D81 Mutation

Zeng, Y.; Johnson, J. L.; Xu, S.; wang, y.

2025-06-07 biophysics
10.1101/2025.06.05.657321 bioRxiv
Show abstract

Protein synthesis relies on accurate mRNA decoding by tRNA, a process guided by EF-Tu. We investigated how mutations at a conserved residue, aspartate 81, affect EF-Tu function using GTPase assays, AlphaFold modeling, and quantum-sensing-based super-resolution force spectroscopy (SURFS). All D81 variants retained GTPase activity but impaired tRNA release, revealed by sub-nucleotide ribosome footprinting. AlphaFold3 modeling suggests that D81 mutations disrupt magnesium coordination and interaction with the sarcin-ricin loop in the GTP-bound state. AlphaFold2-based sequence-structure analysis indicates that D81 anchors coevolutionary constraints, and its mutation enables cryptic structural variation. These results show how a single conserved residue links catalytic coordination, allosteric communication, and evolutionary constraint, offering mechanistic insight into translation fidelity and demonstrating the utility of an unconventional force spectroscopy in probing ribosome dynamics.

Published in Computational and Structural Biotechnology Journal · training set

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