Computational protocol: KRAS insertion mutations are oncogenic and exhibit distinct functional properties

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Protocol publication

[…] K-Ras proteins containing switch 2 duplications were first submitted to the I-TASSER server (http://zhanglab.ccmb.med.umich.edu/I-TASSER/) for structure predictions. The top 10 models showed a diverse set of potential conformations for the inserted sequences (). Although it is difficult to predict the precise orientations of the insertions, the α2-helix (M67-R73) at the C-terminal end of switch 2 maintains helical conformation in each model. In addition, secondary structure prediction indicates that the amino acids immediately preceding the α2-helix (EETSA) have strong helix propensities. Therefore, the insertions are likely to extend the N terminus of the α2-helix, suggesting that the insertions should be more structured than the automatic server predicts. To refine the structure prediction, we used Modeller9v7 (https://salilab.org/modeller/) to create homology models with a published Ras structure (PDB:1WQ1) as the template. For K-RasG60-A66dup, rather than modelling just the insertion sequence (GQEEYSA), the entire 13 amino acid region (QEEYSAGQEEYSA) was modelled in the context of the whole molecule, but without using any structure information from the template. To investigate the potential structural impact of insertion on protein–protein interactions, 20 models were generated. These models all contain an elongated α2-helix and native-like conformations for the disordered regions. Modelling the structure of the 11 amino acid region (QEEYSAEEYSA) in K-RasG62-A66dup using the same approach yielded similar results. […]

Pipeline specifications

Software tools I-TASSER, MODELLER
Application Protein structure analysis
Organisms Mus musculus, Homo sapiens
Diseases Colonic Neoplasms, Neoplasms
Chemicals Amino Acids, Guanosine Triphosphate