The Structural Characterization of Tumor Fusion Genes and Proteins

Computational and Mathematical Methods in Medicine
Dandan WangLu Xie

Abstract

Chromosomal translocation, which generates fusion proteins in blood tumor or solid tumor, is considered as one of the major causes leading to cancer. Recent studies suggested that the disordered fragments in a fusion protein might contribute to its carcinogenicity. Here, we investigated the sequence feature near the breakpoints in the fusion partner genes, the structure features of breakpoints in fusion proteins, and the posttranslational modification preference in the fusion proteins. Results show that the breakpoints in the fusion partner genes have both sequence preference and structural preference. At the sequence level, nucleotide combination AG is preferred before the breakpoint and GG is preferred at the breakpoint. At the structural level, the breakpoints in the fusion proteins prefer to be located in the disordered regions. Further analysis suggests the phosphorylation sites at serine, threonine, and the methylation sites at arginine are enriched in disordered regions of the fusion proteins. Using EML4-ALK as an example, we further explained how the fusion protein leads to the protein disorder and contributes to its carcinogenicity. The sequence and structural features of the fusion proteins may help the scientific com...Continue Reading

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Citations

Jan 5, 2017·Cold Spring Harbor Molecular Case Studies·Vijaykumar R HollaGeorge R Simon
Feb 13, 2021·NAR Genomics and Bioinformatics·Ya CuiWei Li
Mar 29, 2020·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Jian ZhangZunfu Ke

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Methods Mentioned

BETA
X-ray
acetylation

Software Mentioned

MeMo
Pymol
IUPRED
PreDisorder
PredDisorder
PONDR
NetPhos

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