Structure and RNA-binding preferences of the C-terminaldomains of TRIM2 and TRIM3

Abstract

TRIM2 and TRIM3 are two highly homologous members of the tripartite motif (TRIM) protein family. They are primarily expressed in neurons and have roles in cell differentiation and polarisation. Although several roles have been proposed linked to their E3 ligase activity, which is mediated by their N-terminal domains, their proposed role in RNA binding, mediated by their C-terminal NHL domains, has not yet been studied. Here I present an initial characterisation of the RNA binding motif of the TRIM2 and TRIM3 NHL domains, demonstrating that they preferentially bind cytosine rich sequences, put forward a hypothesis as to the likely orientation of the RNA along the top surface of the NHL domain, as well as present structures for the TRIM2 NHL and TRIM3 filamin domains. Additionally, I show a difference in stability between the TRIM2 and TRIM3 NHL domains in solution, which I assessed by biophysical measurements and molecular dynamics simulations. I then explore possible interactions between the NHL and filamin domains and how these might differ between TRIM2 and TRIM3. The results presented show differences in the motif and mode of RNA binding as well as in inter-domain interactions when compared to the well studied homologues of these proteins, Brat and TRIM71.