@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 = {

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.

}, 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} } @article {48725, title = {Thermodynamic modulation of folding and aggregation energy landscape by DNA binding of functional domains of TDP-43}, journal = {Biochimica Et Biophysica Acta-Proteins and Proteomics}, volume = {1871}, year = {2023}, month = {JUL }, pages = {140916}, type = {Article}, abstract = {

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.

}, keywords = {Amyloid-like aggregation, Nucleic acid binding, RNA recognition motifs (RRMs), TDP-43, Thermodynamic stability}, issn = {1570-9639}, doi = {10.1016/j.bbapap.2023.140916}, author = {Patni, Divya and Jha, Santosh Kumar} } @article {49337, title = {DNA-mediated formation of phase-separated coacervates of the nucleic acid-binding domain of TAR DNA-binding protein (TDP-43) prevents its amyloid-like misfolding}, journal = {ACS Chemical Neuroscience}, volume = {15}, year = {2024}, month = {OCT }, pages = {4105-4122}, type = {Article}, abstract = {

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.

}, keywords = {amyloid-likeaggregation, complex coacervation, DNA-protein interactions, Dynamics, pH stress, TDP-43}, issn = {1948-7193}, doi = {10.1021/acschemneuro.4c00117}, author = {Patni, Divya and Patil, Anjali D. and Kirmire, Mona S. and Jha, Anjali and Jha, Santosh Kumar} }