
@article {160486,
	title = {Analyzing sub-millisecond timescale protein dynamics using eCPMG experiments.},
	journal = {J Biomol NMR},
	year = {2025},
	month = {2025 Sep 17},
	abstract = {<p>Cellular functions require biomolecules to transition among various conformational sub-states in the energy landscape. A mechanistic understanding of cellular functions requires quantitative knowledge of the kinetics, thermodynamics, and structural features of the biomolecules experiencing exchange between several states. High-power Relaxation Dispersion (RD) NMR experiments have proven very effective for such measurements if the exchange occurs in timescales ranging from microseconds to milliseconds. However, scanning the significantly larger kinetic window within the time limit of instrumental availability and sample stability requires careful optimization of experiments. Understanding biomolecular functions at a mechanistic level depends on fitting such experimental data to theoretical models. However, the reliability of the fit parameters depends on the measurement schemes and is sensitive to experimental noise. Here, we benchmark different measurement schemes along with theoretical models for sub-millisecond timescale exchange and determine the robustness of these models in providing information when the measurements contain noise. Our results show that kinetics can be measured reliably from such experiments. The structural features of the exchanging sub-states, encoded in the chemical shift differences between the states, can be fitted, albeit with significant uncertainties. Information about the minor states is difficult to obtain exclusively from the RD data due to large uncertainties and sensitivity to noise.</p>
},
	issn = {1573-5001},
	doi = {10.1007/s10858-025-00475-w},
	author = {Phale, Apurva and Tewari, Aishani and Tendulkar, Gayatri and Das, Ranabir and Srinivasan, Sivakumar and Chakrabarti, Kalyan S}
}
@article {16564,
	title = {Conformational Dynamics and Allostery in E2:E3 Interactions Drive Ubiquitination: gp78 and Ube2g2.},
	journal = {Structure},
	year = {2017},
	month = {2017 Apr 13},
	abstract = {<p>Conformational dynamics plays a fundamental role in molecular recognition and activity in enzymes. The ubiquitin-conjugating enzyme (E2) Ube2g2 functions with the ubiquitin ligase (E3) gp78 to assemble poly-ubiquitin chains on target substrates. Two domains in gp78, RING and G2BR, bind to two distant regions of Ube2g2, and activate it for ubiquitin (Ub) transfer. G2BR increases the affinity between the RING and Ube2g2 by 50-fold, while the RING catalyzes the transfer of Ub from the Ube2g2\~{}Ub conjugate. How G2BR and RING activate Ube2g2 is unclear. In this work, conformational dynamics in Ube2g2 revealed a clear correlation of binding G2BR and RING with the sequential progression toward Ub transfer. The interrelationship of the existence and exchange between ground and excited states leads to a dynamic energy landscape model, in which redistribution of populations\&nbsp;contributes to allostery and activation. These findings provide insight into gp78{\textquoteright}s modulation of conformational exchange in Ube2g2 to stimulate ubiquitination.</p>
},
	issn = {1878-4186},
	doi = {10.1016/j.str.2017.03.016},
	author = {Chakrabarti, Kalyan S and Li, Jess and Das, Ranabir and Byrd, R Andrew}
}
