Comparative analysis of sequence-structure function relationship of the SUN-domain protein CaSUN1

Abstract

Sad1/UNC-84 (SUN)-domain proteins are residents of inner nuclear membrane (INM), and share structural features across species. We previously reported a highly conserved C-terminal SUN-domain family protein, designated CaSUN1, in the stress-responsive proteomic landscape of a grain legume, chickpea. In this study, we identified two other chickpea SUN proteins, CaSUN2 and CaSUN3, and performed a comparative analysis of the sequence-structure-function relationship to better understand the diversification of SUN-domain superfamily proteins. Sequence similarity across the species was investigated using multiple sequence alignment, which showed conserved patterns between CaSUN1 and the homologs. Phylogenetic analysis showed that plant SUN-domain proteins are clustered in a unique and distinct group. Using ab-initio approach, a 3D protein structure was generated and further validated using various tools including the Ramachandran plot. The results displayed 90.1% of the à  and à ± residues angles in the most favoured regions, suggesting a high-quality structural model for CaSUN1. Model deviation and fluctuation analysis were performed using molecular dynamics (MD) simulation of CaSUN1. The secondary structure analysis of CaSUN revealed a similarity between the structural components shared among them. CaSUN1 revealed two functional domains viz., SUN and muskelin, and the presence of kelch-repeat domain pointed out its putative role in oligomerization, while its binding affinity with different ligands indicates diverse functions. These results would not only give deeper insights into the structure-function relationships within the SUNsuperfamily proteins, but also their putative physiological roles.