Alternative Conformational Model of a Seed Protein DeK1 for Better Understanding of Structure-Function Relationship

Abstract: Understanding of the cell development and differentiation processes in plant seeds in general is poor. One gene, among others, that predominantly regulates the aleurone cell formation, differentiation and specification in seeds is called defective kernel (DeK1) and several cell biology and genetic experiments have unequivocally established this fact. However, the mechanism behind such processes is still unclear and understanding the protein functionality of DeK1 is vital to elucidating its role in endosperm cell development. Only preliminary investigations have been performed for just one domain of the protein in vitro and its functional implications have been highlighted lately. An initial attempt at in silico modeling of the protein has shown promise and necessitated thorough investigation of the protein to help understand structure-function relationship in details thus corroborating experimental findings and laying foundation for further studies. DeK1 sequences in public databases were used as raw material for elaborate computational analysis of the protein. DeK1 is a multi-pass membrane protein with interesting structural features and the present analysis provides an alternative model for DeK1 structure that can help pan both in vitro and in vivo studies. The transmembrane helices were shown to have a number of conserved charged and polar residues that can form salt bridges and help in ligand binding or transmitting an external signal in addition to maintaining structural integrity. The protein possesses a big loop of about 280-300 amino acid residues on the cytoplasmic side of the membrane. It has a number of putative phosphorylation sites, multiple cysteine residues and a high density of charged residues, all of which could be important for protein-protein interaction and signaling pathways. The loop has a nuclear localization propensity as well. The long C-terminal tail of DeK1 with homology to calpain domain may be activated by the big loop, or conversely the big loop could be a substrate for the calpain protease in addition t