
@article {160488,
	title = {Monitoring Protein Deamidation in Real Time Using NMR.},
	journal = {Magn Reson Chem},
	year = {2025},
	month = {2025 Sep 18},
	abstract = {<p>Deamidation, a modification of glutamine residues in host proteins, plays a key role in bacterial pathogenesis, where bacterial effectors manipulate host signaling pathways by modifying proteins like ubiquitin (Ub) and Ub-like protein NEDD8. The study uses traditional and real-time NMR-based techniques to investigate the enzymatic activity of two bacterial deamidases, cycle inhibitory factors, CIF from Escherichia coli and CIF from Burkholderia pseudomallei. We employed BEST-HSQC NMR spectroscopy to monitor real-time deamidation of ubiquitin, providing a robust and efficient method for quantifying enzyme activity. Our findings highlight significant differences in catalytic efficiency between CIF and CIF, despite their structural similarities. NMR-based rate measurements show CIF has higher catalytic efficiency than CIF, consistent with the previous reports, while kinetic analysis of CIF indicates relatively weak substrate binding and suboptimal efficiency, suggesting a potential regulatory role during infections. While the overall globular fold of the ubiquitin remains unchanged upon deamidation, we observed changes in the local chemical environment, suggesting potential localized structural changes. This study extends the use of NMR spectroscopy to investigate irreversible posttranslational modifications (PTMs) like deamidation, offering a valuable tool for understanding the molecular mechanisms behind bacterial manipulation of host cellular processes.</p>
},
	issn = {1097-458X},
	doi = {10.1002/mrc.70045},
	author = {Agrata, Rashmi and Das, Ranabir}
}
@article {69319,
	title = {Deamidation disrupts native and transient contacts to weaken the interaction between UBC13 and RING-finger E3 ligases.},
	journal = {Elife},
	volume = {8},
	year = {2019},
	month = {2019 Oct 22},
	abstract = {<p>The deamidase OspI from enteric bacteria deamidates a glutamine residue in the host ubiquitin-conjugating enzyme UBC13 and converts it to glutamate (Q100E). Consequently, its polyubiquitination activity in complex with the RING-finger ubiquitin ligase TRAF6 and the downstream NF-κB inflammatory response is silenced. The precise role of deamidation in silencing the UBC13/TRAF6 complex is unknown. We report that deamidation inhibits the interaction between UBC13 and TRAF6 RING-domain (TRAF6) by perturbing both the native and transient interactions. Deamidation creates a new intramolecular salt-bridge in UBC13 that competes with a critical intermolecular salt-bridge at the native UBC13/TRAF6 interface. Moreover, the salt-bridge competition prevents transient interactions necessary to form a typical UBC13/RING complex. Repulsion between E100 and the negatively charged surface of RING also prevents transient interactions in the UBC13/RING complex. Our findings highlight a mechanism wherein a post-translational modification perturbs the conformation and stability of transient complexes to inhibit protein-protein association.</p>
},
	issn = {2050-084X},
	doi = {10.7554/eLife.49223},
	author = {Mohanty, Priyesh and Agrata, Rashmi and Habibullah, Batul Ismail and G S, Arun and Das, Ranabir}
}
