title: Non-canonical pathway network modelling and ubiquitination site prediction through homology modelling of NF-κB.
abstract: Given the fact that NF-κB stays as a dormant molecule in the cytoplasm in steady state, one common step in all the metabolic activities comprising NF-κB is its activation. Consequently there are two pathways of interest related to NF-κB activation: Canonical and alternate. Both the pathways involve ubiquitination of its repressors, that is to say ubiquitination of I-κB by NEMO/IKK-α/IKK-β complex in case of NF-κB1 and that of p100 by IKK-α homodimer in case of NF-κB2. This paper attempts to figure out the ubiquitination sites in alternate pathway of NF-κB activation using a purely computational approach. We initiated the work by acquiring the genes involved in NF kappa B alternate pathway through Agilent literature search. For this we employed the Cytoscape and STRING database. Secondly, the MSA was built using the sequences obtained through BLAST search, and the results were used to update the original sequence list, which was further refined using HMMER. Structural alignment was achieved via Modeller libraries. The final model has been refined using loop_model and asses_dope functions of Modeller. Ubiquitination site is predicted to be comprised of residues 'SPECLDLLVDS' between sites 178 and 188, both positions inclusive. Unlike the classical pathway, due to absence of parallel studies for p100/RelB, a quality match could not be performed, but future studies are in pipeline to replicate the methodology for NF-κB1 activation and compare the results with existing observations. The study can be used to understand the cofactors involved and ubiquitination sites employed during the activation process during drug designing activities. The methodology can be easily scaled and adapted for classical pathway as well.
authors.affiliation: Bioinformatics Division, School of Bio Sciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India.
authors.forename: Sayantan
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: Bioinformatics Division, School of Bio Sciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India. Electronic address: mail2febin@gmail.com.
authors.forename: J
authors.initials: J
authors.lastname: Febin Prabhu Dass
mesh_terms: D000595:Amino Acid Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016328:NF-kappa B / Q000737:chemistry / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D054875:Ubiquitination
chemical_list: D016328:NF-kappa B
keywords: Alternate pathway; Homology modelling; I-κB; IKK-α; MAP3K; NF-κB; NIK; SCFβTrCP/HOS E3 ubiquitin ligase complex; Signalling cross talk; Ubiquitin proteasome signalling system