@article {46196, title = {Slow motion protein dance visualized using red-edge excitation shift of a buried fluorophore}, journal = {Journal of Physical Chemistry B}, volume = {123}, year = {2019}, month = {FEB}, pages = {1256-1264}, type = {Article}, abstract = {

It has been extremely challenging to detect protein structures with a dynamic core, such as dry molten globules, that remain in equilibrium with the tightly packed native (N) state and that are important for a myriad of entropy-driven protein functions. Here, we detect the higher entropy conformations of a human serum protein, using red-edge excitation shift experiments. We covalently introduced a fluorophore inside the protein core and observed that in a subset of native population, the side chains of the polar and buried residues have different spatial arrangements than the mean population and that they solvate the fluorophore on a timescale much slower than the nanosecond timescale of fluorescence. Our results provide direct evidence for the dense fluidity of protein core and show that alternate side-chain packing arrangements exist in the core that might be important for multiple binding functions of this protein.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.8b11151}, author = {Mishra, Prajna and Jha, Santosh Kumar} } @article {48492, title = {Shapeshifter TDP-43: molecular mechanism of structural polymorphism, aggregation, phase separation and their modulators}, journal = {Biophysical Chemistry}, volume = {295}, year = {2023}, month = {APR}, pages = {106972}, type = {Review}, abstract = {

TDP-43 is a nucleic acid-binding protein that performs physiologically essential functions and is known to un-dergo phase separation and aggregation during stress. Initial observations have shown that TDP-43 forms het-erogeneous assemblies, including monomer, dimer, oligomers, aggregates, phase-separated assemblies, etc. However, the significance of each assembly of TDP-43 concerning its function, phase separation, and aggregation is poorly known. Furthermore, how different assemblies of TDP-43 are related to each other is unclear. In this review, we focus on the various assemblies of TDP-43 and discuss the plausible origin of the structural het-erogeneity of TDP-43. TDP-43 is involved in multiple physiological processes like phase separation, aggregation, prion-like seeding, and performing physiological functions. However, the molecular mechanism behind the physiological process performed by TDP-43 is not well understood. The current review discusses the plausible molecular mechanism of phase separation, aggregation, and prion-like propagation of TDP-43.

}, keywords = {Amyloid versus non-amyloid, Coacervation, Environmental conditions, Prion-like seeding, Structural heterogeneity, Thermodynamic and kinetic mechanism}, issn = {0301-4622}, doi = {10.1016/j.bpc.2023.106972}, author = {Doke, Abhilasha A. and Jha, Santosh Kumar} } @article {50072, title = {Structural and mechanistic heterogeneity of the phase separation and aggregation of full-length TDP-43 is governed by environmental conditions}, journal = {ACS Chemical Neuroscience}, volume = {17}, year = {2026}, month = {APR}, pages = {1362-1374}, type = {Article}, abstract = {

TAR DNA-binding protein 43 (TDP-43) is an essential physiological protein implicated in several fatal neurodegenerative disorders. Interestingly, the nature of TDP-43 aggregates varies across patients and disease conditions, suggesting an underlying heterogeneity in its self-assembly behavior. In this study, we investigated two native-like states of full-length TDP-43: the native dimer (N form) and the native-like oligomer (O form). These are compact, folded states with similar secondary structures but differ in size. We found that the N and O forms respond differently to external perturbations and form distinct self-assemblies under stress conditions. Under electrostatic stress, both N and O forms undergo phase separation but produce condensates with markedly different morphologies and dynamics. The underlying mechanisms driving their phase separation are different. Under thermal stress, both forms convert into amyloid aggregates, but again with clearly different morphologies, biochemical properties, and aggregation pathways. These results demonstrate that multiple conformations of TDP-43 respond to distinct perturbations by assembling into structurally and mechanistically different higher-order assemblies. Our findings highlight how the interplay among the structural state, solvation environment, and self-assembly mechanism governs the heterogeneity of TDP-43 assemblies, offering new insights into their physiological roles and pathological relevance. This study suggests that the heterogeneity observed in patients associated with TDP-43 aggregation may arise from differences in the cellular stresses experienced by the protein and the corresponding assembly mechanisms engaged.

}, keywords = {Amyloid-like aggregation, molecular mechanism of phase separation, native-like phase separation, Self-assembly}, issn = {1948-7193}, doi = {10.1021/acschemneuro.5c01003}, author = {Doke, Abhilasha A. and Kirmire, Mona S. and Jha, Anjali and Jha, Santosh Kumar} }