My research focuses on understanding the role of nucleolin (NCL), an RNA-binding protein with extensive post-translational modification, in the DNA damage response. Nucleolin is highly phosphorylated and has been implicated in multiple nuclear processes, including chromatin organization and DNA repair. Despite this, the molecular basis of its interactions within DNA repair pathways remains poorly defined.
To initiate this project, I have begun establishing the computational framework needed to study nucleolin structure and its potential interactions with BRCT-domain–containing proteins involved in DNA repair, such as BRCA1. Early work has focused on becoming proficient with the Schrödinger molecular modeling workflow using the Maestro platform, including structure preparation, visualization, and preliminary modeling approaches relevant to protein–protein and protein–phosphopeptide interactions.
Using available structural models, I have started examining the full-length nucleolin protein, with particular attention to its flexible N-terminal and C-terminal regions and the distribution of known phosphorylation sites. Structural analysis suggests that many phosphorylation sites are located outside of the canonical RNA-binding domains, supporting the idea that phosphorylation may regulate nucleolin’s structural stability or protein–protein interactions rather than its RNA-binding activity. These observations provide a rationale for focusing on phosphorylation-dependent interactions during DNA damage response.
In parallel, I have reviewed known BRCT domain structures and their established role in recognizing phosphorylated peptides during DNA damage signaling. Since nucleolin itself is a phosphoprotein that localizes to sites of DNA damage, this raises the possibility that phosphorylated regions of nucleolin may directly interact with BRCT domains. Current computational efforts are therefore aimed at identifying candidate phosphorylation sites on nucleolin that could serve as potential BRCT-binding motifs.
The computational analyses being developed will directly lead into upcoming experimental work. Planned wet lab experiments include generating phospho-mutant forms of nucleolin, followed by DNA damage assays and cell survival analyses to assess how specific phosphorylation sites influence repair outcomes. These experimental results will be integrated with computational predictions to test how proposed nucleolin–BRCT interactions are functionally relevant in a cellular context.