Biology subjects

Kamariah, N.

Publications and source records attributed to Kamariah, N..

3 recordsLinked to original sources

bioRxiv2026

Molecular Characterization of SARS-CoV-2 N Protein Interfaces: Implications for Oligomerization, RNA Binding, and Phase Separation

The SARS-CoV-2 nucleocapsid (N) protein is central to genomic RNA recognition, condensation, and packaging, yet the molecular organization of its multivalent N-N and N-RNA interaction network involved in this process remains unclear. Here, we define the oligomerization and RNA-binding interfaces of the C-terminal domain (CTD) and its flanking intrinsically disordered regions (IDRs), the leucine-rich helix (LH) and the C-terminal IDR (C-IDR), using size-exclusion chromatography (SEC), cross-linking, mutational studies and NMR spectroscopy. We identify discrete oligomerization interfaces within the CTD and C-IDR that drive higher-order assembly, and show, through liquid-liquid phase separation (LLPS) and electron microscopy (EM), that C-IDR residues are essential for RNA-induced condensate formation. Moreover, the mapping of RNA-binding residues highlights Arg277 as a conserved determinant of CTD-RNA recognition. Notably, the two IDRs exert opposing regulatory effects on RNA binding, with the C-IDR enhancing and the LH attenuating CTD-RNA interactions. Together, these findings reveal how cooperative interfaces between the CTD and its flanking IDRs orchestrate N-protein oligomerization and RNA condensate formation and highlight potential intervention sites for disrupting SARS-CoV-2 ribonucleoprotein assembly.

biophysics↗

bioRxiv2024

Structural and functional insights into nuclear role of Parkinson's Disease-associated α-Synuclein

-Synuclein (Syn) plays a critical role in the pathogenesis of Synucleinopathies. Although increased nuclear Syn localization induces neurotoxicity, its definitive physiological role remains elusive. Previous studies on nuclear Syn are limited to its interactions with individual histones and dsDNA, leaving a significant gap in understanding its interactions with assembled histone H2a-H2b dimer and (H3-H4)2 tetramer, as well as its role in chromatin regulation. Here, we demonstrated that Syn binds specifically to both H2a-H2b and (H3-H4)2 with high affinity. Truncation studies revealed that Syn(1-103) region interacts with (H3-H4)2, while the acidic (121-140) C-terminal end is crucial for H2a-H2b binding. Sequence analysis suggests Syn-dimer binding region contains a conserved DEF/YxP motif present in other dimer-binding histone chaperones. High-resolution structure of Syn- dimer binding region with H2a-H2b complex reveals that Syn adopts two binding modes (BM1 and BM2). In BM-1, Syn utilizes nucleosomal DNA-binding surface, while in BM-2, it engages with both DNA- and the H3-interaction interface. Additionally, dimer recognition by Syn overlaps with other dimer-binding histone chaperones, suggesting Syns potential role in the nucleosome assembly/disassembly process.

biophysics↗

bioRxiv2021

Inhibition of HIV-1 immune modulation by small molecules targeting viral Nef-host CD80 interface

HIV-1 causes diverse immunomodulatory responses in the host, including the down-regulation of co-stimulatory proteins CD80/86, mediated by HIV-1 protein Nef, blunting T-cell activation. Using a screening cascade of biochemical and cell-based assays, we identified potent small molecules representing three chemical scaffolds namely amino pyrimidine, phenoxy acetamide and bi-aryl heteroaryl carbamate which target the protein-protein interaction interface of CD80/86 and Nef with sub-micromolar potency. These molecules restore CD80/86 surface levels in HIV-1-Nef infected antigen presenting cells and T-cell activation. Nef-CD80 interface and small molecule binding sites were mapped by using computational docking and structural studies, followed by validation by mutational analysis. This analysis resulted in the identification of two key residues, K99 and R111, which were associated with down-modulation of CD80 surface levels by Nef and important for small molecule binding. Targeting these interacting residues disabled Nef-mediated down-modulation of CD80 surface levels, consequently restoring T-cell activation. Thus, we validate a new target, the Nef-CD80/86 protein-protein interaction interface, with a potential to develop new inhibitors to counteract the immunomodulatory consequences of HIV-1.

microbiology↗