@article { ISI:000340538400005, title = {Subtilase from Beauveria sp.: conformational and functional investigation of unusual stability}, journal = {European Biophysics Journal With Biophysics Letters}, volume = {43}, number = {8-9}, year = {2014}, month = {SEP}, pages = {393-403}, publisher = {SPRINGER}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

Retention of total activity of the subtilisin-like serine protease from Beauveria sp. MTCC 5184 (Bprot) in the vicinity of (1) 3 M GdnHCl for 12 h, (2) 50 \% methanol and dimethyl sulfoxide each for 24 h, and (3) proteolytic enzymes (trypsin, chymotrypsin, and proteinase K) for 48 h led to expect the enzyme to be a kinetically stable protein. Also, the structure of the protein was stable at pH 2.0. Biophysical characterization and conformational transitions were monitored using steady-state and time-resolved fluorescence, FTIR, and CD spectroscopy. Single tryptophan in the protein exists as two conformers, in hydrophobic and polar environment. The secondary structure of Bprot was stable in 3 M GdnHCl as seen in far-UV CD spectra. The active fraction of Bprot obtained from size-exclusion chromatography in the presence of GdnHCl (1.0-3.0 M) eluted at reduced retention time. The peak area of inactive or denatured protein with the same retention time as that of native protein increased with increasing concentration of denaturant (1.0-4.0 M GdnHCl). However, the kinetics of GdnHCl-induced unfolding as studied from intrinsic fluorescence revealed k (unf) of native protein to be 5.407 x 10(-5) s(-1) and a half-life of 3.56 h. The enzyme is thermodynamically stable in spite of being resistant to the denaturant, which could be due to the effect of GdnHCl imparting rigidity to the active fraction and simultaneously unfolding the partially unfolded protein that exists in equilibrium with the folded active protein. Thermal and pH denaturation of Bprot exhibited interesting structural transitions.

}, keywords = {Beauveria, Chemical denaturation, Conformational transitions, Serine protease, Subtilase, Thermal denaturation, Thermodynamic stability}, issn = {0175-7571}, doi = {10.1007/s00249-014-0971-z}, author = {Dalal, Sayli A. and More, Snehal V. and Shankar, Shiv and Laxman, Ryali Seeta and Gaikwad, Sushama M.} } @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 {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} }