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

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.

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-residue02040nas a2200157 4500008004100000022001400041245011600055210006900171260000900240300001400249490000800263520144100271100001701712700002401729856012901753 2021 eng d a1520-610600aProtonation-deprotonation switch controls the amyloid-like misfolding of nucleic-acid-binding domains of TDP-430 aProtonationdeprotonation switch controls the amyloidlike misfold cAUG  a8383-83940 v1253 aNutrient 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.1 aPatni, Divya1 aJha, Santosh, Kumar uhttps://library.ncl.res.in/content/protonation-deprotonation-switch-controls-amyloid-misfolding-nucleic-acid-binding-domains02235nas 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

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.

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-functional02380nas a2200265 4500008004100000022001400041245016600055210006900221260000900290300001400299490000700313520144700320653002801767653002501795653002901820653001301849653001401862653001101876100001701887700002201904700002201926700001601948700002401964856012601988 2024 eng d a1948-719300aDNA-mediated formation of phase-separated coacervates of the nucleic acid-binding domain of TAR DNA-binding protein (TDP-43) prevents its amyloid-like misfolding0 aDNAmediated formation of phaseseparated coacervates of the nucle cOCT  a4105-41220 v153 a

Sequestration of protein molecules and nucleic acids to stress granules is one of the most promising strategies that cells employ to protect themselves from stress. In vitro, studies suggest that the nucleic acid-binding domain of TDP-43 (TDP-43tRRM) undergoes amyloid-like aggregation to beta-sheet-rich structures in low pH stress. In contrast, we observed that the TDP-43tRRM undergoes complex coacervation in the presence of ssDNA to a dense and light phase, preventing its amyloid-like aggregation. The soluble light phase consists of monomeric native-like TDP-43tRRM. The microscopic data suggest that the dense phase consists of spherical coacervates with limited internal dynamics. We performed multiparametric analysis by employing various biophysical techniques and found that complex coacervation depends on the concentration and ratio of the participating biomolecules and is driven by multivalent interactions. The modulation of these forces due to environmental conditions or disease mutations regulates the extent of coacervation, and the weakening of interactions between TDP-43tRRM and ssDNA leads to amyloid-like aggregation of TDP-43tRRM. Our results highlight a competition among the native state, amyloid-like aggregates, and complex coacervates tuned by various environmental factors. Together, our results illuminate an alternate function of TDP-43tRRM in response to pH stress in the presence of the ssDNA.

10aamyloid-likeaggregation10acomplex coacervation10aDNA-protein interactions10aDynamics10apH stress10aTDP-431 aPatni, Divya1 aPatil, Anjali, D.1 aKirmire, Mona, S.1 aJha, Anjali1 aJha, Santosh, Kumar uhttps://library.ncl.res.in/content/dna-mediated-formation-phase-separated-coacervates-nucleic-acid-binding-domain-tar-dna