Publications of NIPGR Scientists

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Subject: search.filters.subject.Multiple sequence alignment

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    Comparative analysis of sequence-structure function relationship of the SUN-domain protein CaSUN1
    (OMICS International, 2017) Mishra, Poonam; Wardhan, Vijay; Pandey, Aarti; Chakraborty, Subhra; Garg, Gunjan; Chakraborty, Niranjan
    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.
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    Genome wide in silico characterization of Dof transcription factor gene family of sugarcane and its comparative phylogenetic analysis with Arabidopsis, rice and sorghum
    (Springer, 2014) Gupta, Shubhra; Kushwaha, Hariom; Singh, Vinay Kumar; Bisht, Naveen C.; Sarangi, Bijaya Ketan; Yadav, Dinesh
    A total of 25 Dof genes were retrieved from GRASSIUS grass regulatory information server. These sequences were in silico characterized for homology search, multiple sequence alignment for conserved Dof DNA binding domains, distribution of conserved motifs and phylogenetic relatedness with sorghum, rice and Arabidopsis. A highly conserved four cysteine residues associated with typical zinc finger of Dof family was observed on multiple sequence alignment of Dof domains. A highly conserved cysteine residue at positions 3 and 6 along with proline and sulfur at positions 4 and 8, respectively were observed. The phylogenetic tree of 119 Dof protein sequences of sugarcane, rice, sorghum and Arabidopsis revealed ten distinct clades with several orthologs and paralogs. The distributions of 25 conserved motifs were analyzed for Dof proteins of sugarcane. Dof proteins with closely related members in the phylogenetic tree shared common motif distribution revealing the possibility of functional similarities within the same subgroup. The motif 1 representing the conserved Dof domain of 50 amino acids was uniformly observed in all the Dof proteins of sugarcane except ScDof8 and ScDof14.