01700nas a2200157 4500008004100000245010000041210006900141260000800210300001600218490000700234520111600241100002101357700001901378700002401397856012101421 2017 eng d00aDry molten globule-like intermediate during the base-induced unfolding of a multidomain protein0 aDry molten globulelike intermediate during the baseinduced unfol cNOV a30207-302160 v193 aThe 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.1 aAcharya, Nirbhik1 aMishra, Prajna1 aJha, Santosh, Kumar uhttps://library.ncl.res.in/content/dry-molten-globule-intermediate-during-base-induced-unfolding-multidomain-protein00607nas a2200145 4500008004100000245012500041210006900166260000800235300001600243490000700259100002100266700001900287700002400306856013100330 2019 eng d00aDry molten globule-like intermediate during the base-induced unfolding of a multidomain protein (vol 19, pg 20307, 2017)0 aDry molten globulelike intermediate during the baseinduced unfol cSEP a20499-204990 v211 aAcharya, Nirbhik1 aMishra, Prajna1 aJha, Santosh, Kumar uhttps://library.ncl.res.in/content/dry-molten-globule-intermediate-during-base-induced-unfolding-multidomain-protein-vol-19-pg01426nas a2200157 4500008004100000022001400041245008400055210006900139260000800208300001400216490000800230520087600238100002101114700002401135856010901159 2022 eng d a1520-610600aDry molten globule-like intermediates in protein folding, function, and disease0 aDry molten globulelike intermediates in protein folding function cNOV a8614-86220 v1263 a

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.

1 aAcharya, Nirbhik1 aJha, Santosh, Kumar uhttps://library.ncl.res.in/content/dry-molten-globule-intermediates-protein-folding-function-and-disease02962nas a2200277 4500008004100000022001400041245013400055210006900189260000800258300001400266490000700280520195400287653002502241653002702266653002802293653003202321653002502353653003002378653003602408653002302444100002302467700002402490700002402514700001502538856013102553 2024 eng d a1948-719300aDeciphering the monomeric and dimeric conformational landscapes of the full-length TDP-43 and the impact of the C-terminal domain0 aDeciphering the monomeric and dimeric conformational landscapes  cNOV a4305-43210 v153 a

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.

10achain collapsibility10adomain-wisefluctuation10aelectrostatic dominance10ahydrogen bond switchability10along-range crosstalk10apersistent beta-character10aprotagonistic C-terminal domain10arugged phase space1 aTammara, Vaishnavi1 aDoke, Abhilasha, A.1 aJha, Santosh, Kumar1 aDas, Atanu uhttps://library.ncl.res.in/content/deciphering-monomeric-and-dimeric-conformational-landscapes-full-length-tdp-43-and-impact-c02380nas 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