Database of length variant protein domains

Protein domains are the functional and evolutionary units of protein structure and are independent in its functionality and folding pattern. These protein domains (across certain protein folds) has the ability to tolerate changes in sequence and length during evolutionary drifts, without changing its folding topology or functionality. Length variations at protein domain level have been known to cause functional impacts like, increasing structural stability, diversifying substrate specificity etc. A comprehensive resource of length variant protein domains at superfamily level (LenVarDB) will help users solve issues like; will the presence of length variations hinder substrate entry by formation of a capping loop or will they form a new interface and diversify the social skills of a protein domain? Though these variations have been recorded only at the level of protein domain "structures", this database attempts (for the first time) to include sequence information, by gathering homologues of superfamily members and deriving indels from their multiple sequence alignment. Detection of multiple length variants (indels) along with their spatial orientation in a given query protein structure, could be very useful in highlighting the deviations caused from its usual structure and function. Users can also align their query proteins with the existing multiple sequence alignments to trace putative indel positions. Insight into the indel locations whether they are proximal or distant from the functionally relevant sites can provide pointers to probable changes in functionality of their protein or tips in modeling and structural studies.

Please cite us: Mutt, E., Mathew, O. K., Sowdhamini, R., Jan. 2014. LenVarDB: database of length-variant protein domains. Nucleic Acids Research 42 (D1), D246-D250. URL http://dx.doi.org/10.1093/nar/gkt1014

BIOLOGICAL SIGNIFICANCE: Length variations (indels) are instrumental in causing changes in protein structure and function (Zhang et. al.,MBE,2010). They have also been implicated in disease related genes (Kim et. al., Journal of Genetics, 2012). Protein domain superfamilies having long length variations found to be interacting with diverse substrates and were also found to be in various oligomeric states.(Sandhya et.al., PlosONE, 2009)

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