Non-canonical pathway network modelling and ubiquitination site prediction through homology modelling of NF-κB

Gene
Sayantan Ghosh, J Febin Prabhu Dass

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. Un...Continue Reading

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Citations

Apr 4, 2019·American Journal of Physiology. Renal Physiology·May M RabadiH Thomas Lee
May 2, 2019·Frontiers in Immunology·Ning SongLinlin Guo
Jul 2, 2021·Frontiers in Immunology·Aidil ZainiSebastian Scheer

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