@article {49216, title = {Characterization of the conformational hotspots of the RNA-dependent RNA polymerase complex identifies a unique structural malleability of nsp8}, journal = {Journal of Physical Chemistry B}, volume = {128}, year = {2024}, month = {OCT }, pages = {9959-9975}, type = {Article}, abstract = {

Several antiviral therapeutic approaches have been targeted toward the RNA-dependent RNA polymerase (RdRp) complex that is involved in viral genome replication. In SARS-CoV-2, although the RdRp is a multiprotein complex, the focus has been on the ligand binding catalytic core (nonstructural protein nsp12), and not the multiprotein functional dynamics. In this study, we focus on the conformational ensembles of the RdRp complex and their modulation by the presence of RNA, performing comprehensive microsecond-scale atomistic simulations of the apo- and RNA-bound complex. We delineate the differential impact of RNA on the constituent proteins, such as conformational polymorphisms, dominant segment-specific fluctuations, and the switch in dynamical crosstalk within the complex. We distinguish dynamical signatures of nsp7, nsp8, and nsp12 in the apo-state that are reduced in the presence of the RNA and appear to {\textquoteleft}{\textquoteleft}prime{\textquoteright}{\textquoteright} the complex for activity. Importantly, we identify a unique structural malleability of the nsp8 protein with high conformational heterogeneity in the apo state, especially at three sites (Y71 for nsp8A, and D52 and A66 for nsp8B). Our work highlights the functional implications of the polymorphism of nsp8 structures and reveals possibilities for the development of allosteric inhibitors.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.4c03851}, author = {Gharui, Sowmomita and Sengupta, Durba and Das, Atanu} } @article {49414, title = {Molecular interactions of the pioneer transcription factor GATA3 With DNA}, journal = {Proteins-Structure Function and Bioinformatics}, volume = {93}, year = {2025}, month = {FEB}, pages = {555-566}, type = {Article}, abstract = {

The GATA3 transcription factor is a pioneer transcription factor that is critical in the development, proliferation, and maintenance of several immune cell types. Identifying the detailed conformational dynamics and interactions of this transcription factor, as well as its clinically important population variants will allow us to unravel its mode of action. In this study, we analyze the molecular interactions of the GATA3 transcription factor bound to dsDNA as well as three clinically important population variants by atomistic molecular dynamics simulations. We identify the effect of the variants on the DNA conformational dynamics and delineate the differences compared to the wildtype transcription factor that could be related to impaired function. We highlight the structural plasticity in the binding of the GATA3 transcription factor and identify important DNA-protein contacts. Although the DNA-protein contacts are persistent and appear to be stable, they exhibit nanosecond timescale fluctuations and several binding/unbinding events. Further, we identify differential DNA binding in the three variants and show that the N-terminal binding is reduced in two of the variants. Our results indicate that reduced minor groove width and DNA diameter are important hallmarks for the binding of GATA3. Our work is an important step towards understanding the functional dynamics of the GATA3 protein and its clinically significant population variants.

}, keywords = {DNA-protein interactions, GATA protein, Molecular dynamics simulations, molecular mechanism, population variants, transcription factor}, issn = {0887-3585}, doi = {10.1002/prot.26749}, author = {Gharui, Sowmomita and Sengupta, Durba} } @article {50149, title = {Recognition of diverse GATA motifs necessitates multimodal GATA3-DNA binding}, journal = {Biochemical and Biophysical Research Communications}, volume = {817}, year = {2026}, month = {JUN}, pages = {153718}, type = {Article}, abstract = {

GATA3 is a pioneer transcription factor that plays a central role in the formation, proliferation, and sustenance of various immune cell types, notably serving as the {\textquoteleft}{\textquoteleft}master regulator{\textquoteright}{\textquoteright} of T helper 2 (Th2) cell differentiation. It regulates gene expression by recognizing the canonical DNA consensus motif (A/T)GATA(A/G) through its highly conserved zinc finger domains. However, beyond this classical binding motif, emerging evidence indicates that GATA3 also recognizes a varied array of noncanonical and palindromic sequence motifs, but the underlying molecular mechanisms are unclear. In this review, we discuss an emerging aspect of GATA3 function that links these diverse DNA sequence motifs to varying structural binding modes and finally to differential chromatin outcomes. We discuss how the alternative sequence motifs may engage the two zinc finger domains differently, leading towards a multitude of binding modes underlying this diverse motif recognition. The spacer length between the GATA motifs has been shown to modulate DNA binding and the geometric constraints imposed may help determine the binding mode. We reanalyzed previous data and show that these diverse motifs, as well as the spacers, modulate nucleosomal outcomes, highlighting the importance of these motifs in GATA3 function. Several disease-associated mutations, such as those implicated in autoimmune diseases and cancer, have been reported for GATA3, and we discuss how these mutations alter the binding of the zinc finger domains. This link between sequence recognition and DNA binding modes represents an underexplored aspect of GATA3 function that is necessary for understanding its multifaceted regulatory role in human health and disease.

}, keywords = {GATA, Mutations, Nucleosome, Palindrome, Reverse palindrome, Spacers, Tandem}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2026.153718}, author = {Gharui, Sowmomita and Puntambekar, Shraddha and Sarkar, Ram Rup and Narlikar, Leelavati and Sengupta, Durba} }