Institutional Publications

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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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    Dissecting the chloroplast proteome of chickpea (Cicer arietinum L.) provides new insights into classical and non-classical functions
    (Elsevier B.V., 2017) Lande, Nilesh Vikram; Subba, Pratigya; Barua, Pragya; Gayen, Dipak; Keshava Prasad, T.S.; Chakraborty, Subhra; Chakraborty, Niranjan
    Chloroplast, the energy organelle unique to plant cells, is a dynamic entity which integrates an array of metabolic pathways and serves as first level for energy conversion for the entire ecological hierarchy. Increasing amount of sequence data and evolution of mass spectrometric approaches has opened up new avenues for opportune exploration of the global proteome of this organelle. In our study, we aimed at generation of a comprehensive catalogue of chloroplast proteins in a grain legume, chickpea and provided a reference proteome map. To accurately assign the identified proteins, purity of chloroplast-enriched fraction was stringently monitored by multiple chemical and immunological indexes, besides pigment and enzyme analyses. The proteome analysis led to the identification of 2451 proteins, including 27 isoforms, which include predicted and novel chloroplast constituents. The identified proteins were validated through their sequence analysis. Extensive sequence based localization prediction revealed more than 50% proteins to be chloroplast resident by at least two different algorithms. Chromosomal distribution of identified proteins across nuclear and chloroplast genome unveiled the presence of 55 chloroplast encoded gene. In depth comparison of our dataset with the non-redundant set of chloroplast proteins identified so far across other species revealed novel as well as overlapping candidates.
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    Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum L.)
    (BioMed Central, 2012) Jaiswal, Dinesh Kumar; Ray, Doel; Subba, Pratigya; Mishra, Poonam; Gayali, Saurabh; Datta, Asis; Chakraborty, Subhra; Chakraborty, Niranjan
    Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades.