@article {44095, title = {Dry molten globule-like intermediate during the base-induced unfolding of a multidomain protein}, journal = {Physical Chemistry Chemical Physics}, volume = {19}, year = {2017}, month = {NOV}, pages = {30207-30216}, type = {Article}, abstract = {The nature of the initial structural events during the base-induced unfolding of the native (N) state of proteins is poorly understood. Combining site-specific fluorescence resonance energy transfer, size exclusion chromatography, dynamic fluorescence quenching, red-edge excitation shift and circular dichroism spectroscopy, we show here that an early intermediate during the base-induced unfolding of a multidomain protein, i.e., the B form, has features of a dry molten globule. We show that the N (sic) B transition involves protein expansion and loosening of packing of inter-domain helices near domains I and II without the disruption of intra-domain packing or any change in hydration of the inter-domain region which resembles a molten hydrocarbon. Surprisingly, the disruption of inter-domain packing accounts for 40-45\% of the total change in free energy of complete unfolding. Our results show that the disruption of van der Waals packing can be decoupled in different regions of a protein and could occur prior to hydrophobic solvation during base-induced unfolding, challenging the existing notion.}, doi = {10.1039/c7cp06614g}, author = {Acharya, Nirbhik and Mishra, Prajna and Jha, Santosh Kumar} } @article {46274, title = {Dry molten globule-like intermediate during the base-induced unfolding of a multidomain protein (vol 19, pg 20307, 2017)}, journal = {Physical Chemistry Chemical Physics}, volume = {21}, year = {2019}, month = {SEP}, pages = {20499-20499}, type = {Correction}, doi = {10.1039/c9cp90219h}, author = {Acharya, Nirbhik and Mishra, Prajna and Jha, Santosh Kumar} } @article {48016, title = {Dry molten globule-like intermediates in protein folding, function, and disease}, journal = {Journal of Physical Chemistry B}, volume = {126}, year = {2022}, month = {NOV}, pages = {8614-8622}, type = {Review}, abstract = {

The performance of a protein depends on its correct folding to the final functional native form. Hence, understanding the process of protein folding has remained an important field of research for the scientific community for the past five decades. Two important intermediate states, namely, wet molten globule (WMG) and dry molten globule (DMG), have emerged as critical milestones during protein folding-unfolding reactions. While much has been discussed about WMGs as a common unfolding intermediate, the evidence for DMGs has remained elusive owing to their near-native features, which makes them difficult to probe using global structural probes. This Review puts together the available literature and new evidence on DMGs to give a broader perspective on the universality of DMGs and discuss their significance in protein folding, function, and disease.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.2c04991}, author = {Acharya, Nirbhik and Jha, Santosh Kumar} } @article {49250, title = {Deciphering the monomeric and dimeric conformational landscapes of the full-length TDP-43 and the impact of the C-terminal domain}, journal = {ACS Chemical Neuroscience}, volume = {15}, year = {2024}, month = {NOV}, pages = {4305-4321}, type = {Article}, abstract = {

The aberrant aggregation of TAR DNA-binding protein 43 kDa (TDP-43) in cells leads to the pathogenesis of multiple fatal neurodegenerative diseases. Decoding the proposed initial transition between its functional dimeric and aggregation-prone monomeric states can potentially design a viable therapeutic strategy, which is presently limited by the lack of structural detail of the full-length TDP-43. To achieve a complete understanding of such a delicate phase space, we employed a multiscale simulation approach that unearths numerous crucial features, broadly summarized in two categories: (1) state-independent features that involve inherent chain collapsibility, rugged polymorphic landscape dictated by the terminal domains, high beta-sheet propensity, structural integrity preserved by backbone-based intrachain hydrogen bonds and electrostatic forces, the prominence of the C-terminal domain in the intrachain cross-domain interfaces, and equal participation of hydrophobic and hydrophilic (charged and polar) residues in cross-domain interfaces; and (2) dimerization-modulated characteristics that encompass slower collapsing dynamics, restricted polymorphic landscape, the dominance of side chains in interchain hydrogen bonds, the appearance of the N-terminal domain in the dimer interface, and the prominence of hydrophilic (specifically polar) residues in interchain homo- and cross-domain interfaces. In our work, the ill-known C-terminal domain appears as the most crucial structure-dictating domain, which preferably populates a compact conformation with a high beta-sheet propensity in its isolated state stabilized by intrabackbone hydrogen bonds, and these signatures are comparatively faded in its integrated form. Validation of our simulated observables by a complementary spectroscopic approach on multiple counts ensures the robustness of the computationally predicted features of the TDP-43 aggregation landscape.

}, keywords = {chain collapsibility, domain-wisefluctuation, electrostatic dominance, hydrogen bond switchability, long-range crosstalk, persistent beta-character, protagonistic C-terminal domain, rugged phase space}, issn = {1948-7193}, doi = {10.1021/acschemneuro.4c00557}, author = {Tammara, Vaishnavi and Doke, Abhilasha A. and Jha, Santosh Kumar and Das, Atanu} } @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} }