02266nas a2200217   4500008004100000022001400041245010100055210006900156260000800225300001100233490000800244520150100252653003101753653003001784653002801814653002201842100001901864700001701883700002401900856012401924       2021                        eng d  a0301-462200apH-dependent protein stability switch coupled to the perturbed pKa of a single ionizable residue0 apHdependent protein stability switch coupled to the perturbed pK  cJUL  a1065910 v2743 a<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>10aelectrostatic interactions10aFluorescence spectroscopy10aThermodynamic stability10aUnfolded proteins1 aMishra, Prajna1 aPatni, Divya1 aJha, Santosh, Kumar  uhttps://library.ncl.res.in/content/ph-dependent-protein-stability-switch-coupled-perturbed-pka-single-ionizable-residue02235nas a2200217   4500008004100000022001400041245012000055210006900175260000900244300001100253490000900264520144800273653002901721653002501750653003401775653001101809653002801820100001701848700002401865856012801889       2023                        eng d  a1570-963900aThermodynamic modulation of folding and aggregation energy landscape by DNA binding of functional domains of TDP-430 aThermodynamic modulation of folding and aggregation energy lands  cJUL   a1409160 v18713 a<p>
	TDP-43 is a vital nucleic acid binding protein which forms stress-induced aberrant aggregates in around 97% cases of ALS, a fatal neurodegenerative disease. The functional tandem RRM domain of the protein (TDP-43tRRM) has been shown to undergo amyloid-like aggregation under stress in a pH-dependent fashion. However, the underlying thermodynamic and molecular basis of aggregation and how the energy landscape of folding, stability, and aggregation are coupled and modulated by nucleic acid binding is poorly understood. Here, we show that the pH stress thermodynamically destabilizes the native protein and systematically populates the unfoldedlike aggregation-prone molecules which leads to amyloid-like aggregation. We observed that specific DNA binding inhibits aggregation and populates native-like compact monomeric state even under low-pH stress as measured by circular dichroism, ANS binding, size exclusion chromatography, and transmission electron microscopy. We show that DNA-binding thermodynamically stabilizes and populates the native state even under stress and reduces the population of unfolded-like aggregation-prone molecules which leads to systematic aggregation inhibition. Our results suggest that thermodynamic modulation of the folding and aggregation energy landscape by nucleic-acid-like molecules could be a promising approach for effective therapeutic intervention in TDP-43-associated proteinopathies.</p>
10aAmyloid-like aggregation10aNucleic acid binding10aRNA recognition motifs (RRMs)10aTDP-4310aThermodynamic stability1 aPatni, Divya1 aJha, Santosh, Kumar  uhttps://library.ncl.res.in/content/thermodynamic-modulation-folding-and-aggregation-energy-landscape-dna-binding-functional