Team:Lethbridge/Model
MODEL
While VLPs will be useful components of VINCEnT, we wanted to focus on development of a novel non-immunogenic PNC with RNA packaging capabilities. Such a tool could enable simpler transfection of mammalian cell lines for fellow iGEMers and other researchers.
To do this, we identified the Rattus norvegicus Arc protein as a candidate for modelling a minimal packaging protein. Arc is an activity-regulated cytoskeletal-associated protein that has recently been recognized as a repurposed Ty3/Gypsy retrotransposon. A bi-lobar domain within Arc has significant homology to Gag proteins, which are the major capsid proteins of many viruses including Human Immunodeficiency Virus type 1 (HIV-1), Rous-Sarcoma Virus (RSV), and Bovine Leukemia Virus (BLV). In response to synaptic activity in neurons, Arc proteins self-assemble via this Gag domain (similar to the related viral particles) to encapsulate Arc mRNA and shuttle it to neighbouring cells (Pastuzyn et al., 2018; Ashley et al., 2018).
To ensure we would not retain any native Arc functionality that might impact cellular activity, we designed a “minimal” Arc Gag protein based on homology with other known Gag domains. We used template-based structural predictions to model this minimal Arc Gag and its predicted assembly into higher-order structures.
SEQUENCE DESIGN
Using the EMBL-EBI Clustal Omega tool,we aligned the protein sequences of HIV-1 (GenBank BAF32552.1), BLV (GenBank BAA00543.1), and RSV (PDB 5A9E) Gag proteins to R. norvegicus Arc (NCBI Ref NP_062234.1). The most closely conserved sequences are shown below:
Based on HIV-1 homology to Arc, Zhang et al. (2015) similarly predicted a conserved Gag domain to span R. norvegicus Arc amino acids 207-278 (Gag N-lobe) and 278-370 (Gag C-lobe).