Poly(rC) Binding Protein (PCBPs) are triple hnRNP K (KH) domain proteins involved in post-transcriptional regulation. PCBPs bind to cytosine rich tracts of ssRNA/ssDNA via KH domains for translational activation, silencing and mRNA stability. PCBPs are also hijacked by viruses and recruited to assist with viral replication.
The understanding of how PCBPs are able to recognise C-rich oligonucleotides and exhibit diverse functions is much sought after. In order to understand binding of PCBP to ssDNA/ssRNA targets, I have used both computational and experimental approaches to determine preferred oligonucleotide sequences and also to better understand the binding affinity of KH domains to C-rich oligonucleotides.
Structures of PCBP KH domains provided a basis for computational investigations such as molecular dynamics to define interactions between protein and nucleic acid structures. Amino acid residues that were thought to contribute to protein-nucleic acid binding were then mutated in order to observe their effects on binding. Binding affinity was calculated by monitoring protein-DNA interactions with the use of biosensors (SPR) in real time, as well as the use of fluorescence anisotropy. Overall, we have arrived at a better understanding of PCBP recognition of C-rich oligonucleotides.