@article {47344,
	title = {pH-dependent protein stability switch coupled to the perturbed pKa of a single ionizable residue},
	journal = {Biophysical Chemistry},
	volume = {274},
	year = {2021},
	month = {JUL},
	pages = {106591},
	type = {Article},
	abstract = {<p>The contribution of electrostatic interactions in protein stability has not been fully understood. Burial of an ionizable amino acid inside the hydrophobic protein core can affect its ionization equilibrium and shift its pKa differentially in the native (N) and unfolded (U) states of a protein and this coupling between the folding/ unfolding cycle and the ionization equilibria of the ionizable residue can substantially influence the protein stability. Here, we studied the coupling of the folding/unfolding cycle with the ionization of a buried ionizable residue in a multi-domain protein, Human Serum Albumin (HSA) using fluorescence spectroscopy. A pHdependent change in the stability of HSA was observed in the near native pH range (pH 6.0-9.0). The protonation-deprotonation equilibrium of a single thiol residue that is buried in the protein structure was identified to give rise to the pH-dependent protein stability. We quantified the pKa of the thiol residue in the N and the U states. The mean pKa of the thiol in the N state was upshifted by 0.5 units to 8.7 due to the burial of the thiol in the protein structure. Surprisingly, the mean pKa of the thiol in the U state was observed to be downshifted by 1.3 units to 6.9. These results indicate that some charged residues are spatially proximal to the thiol group in the U state. Our results suggest that, in addition to the N state, electrostatic interactions in the U state are important determinants of protein stability.</p>},
	keywords = {electrostatic interactions, Fluorescence spectroscopy, Thermodynamic stability, Unfolded proteins},
	issn = {0301-4622},
	doi = {10.1016/j.bpc.2021.106591},
	author = {Mishra, Prajna and Patni, Divya and Jha, Santosh Kumar}
}
@article {47663,
	title = {Protonation-deprotonation switch controls the amyloid-like misfolding of nucleic-acid-binding domains of TDP-43},
	journal = {Journal of Physical Chemistry B},
	volume = {125},
	year = {2021},
	month = {AUG },
	pages = {8383-8394},
	type = {Article},
	abstract = {Nutrient starvation stress acidifies the cytosol and leads to the formation of large protein assemblies and misfolded aggregates. However, how starvation stress is sensed at the molecular level and leads to protein misfolding is poorly understood. TDP-43 is a vital protein, which, under stress-like conditions, associates with stress granule proteins via its functional nucleic-acid-binding domains (TDP-43(t)(RRM)) and misfolds to form aberrant aggregates. Here, we show that the monomeric N form of TDP-43(t)(RRM) forms a misfolded amyloid-like protein assembly, beta form, in a pH-dependent manner and identified the critical protein side-chain residue whose protonation triggers its misfolding. We systematically mutated the three buried ionizable residues, D105, H166, and H256, to neutral amino acids to block the pH-dependent protonation-deprotonation titration of their side chain and studied their effect on the N-to-beta transition. We observed that D105A and H2S6Q resembled TDP-43(t)(RRM) in their pH-dependent misfolding behavior. However, H166Q retains the N-like secondary structure under low-pH conditions and does not show pH-dependent misfolding to the beta form. These results indicate that H166 is the critical side-chain residue whose protonation triggers the misfolding of TDP-43(t)(RRM) and shed light on how stress-induced misfolding of proteins during neurodegeneration could begin from site-specific triggers.},
	issn = {1520-6106},
	doi = {10.1021/acs.jpcb.1c03262},
	author = {Patni, Divya and Jha, Santosh Kumar}
}
