Functional and structural analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the MYB oncoproteins associated with human cancer

Abstract

MYB proteins are highly conserved DNA-binding domains (DBD) and mutations in MYB oncoproteins have been reported to cause aberrant and augmented cancer progression. Identification of MYB molecular biomarkers predictive of cancer progression can be used for improving cancer management. To address this, a biomarker discovery pipeline was employed in investigating deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in predicting damaging and potential alterations on the properties of proteins. The nsSNP of the MYB family; MYB, MYBL1, and MYBL2 was extracted from the NCBI database. Five in silico tools (PROVEAN, SIFT, PolyPhen-2, SNPs&GO and PhD-SNP) were utilized to investigate the outcomes of nsSNPs. A total of 45 nsSNPs were predicted as high-risk and damaging, and were subjected to PMut and I-Mutant 2.0 for protein stability analysis. This resulted in 32 nsSNPs with decreased stability with a DDG score lower than - 0.5, indicating damaging effect. G111S, N183S, G122S, and S178C located within the helix-turn-helix (HTH) domain were predicted to be conserved, further posttranslational modifications and 3-D protein analysis indicated these nsSNPs to shift DNA-binding specificity of the protein thus altering the protein function. Findings from this study would help in the field of pharmacogenomic and cancer therapy towards better intervention and management of cancer.

Figure 1

Putative PTM sites and high risk nsSNPs in MYB family proteins. (a) MYB had 90 common phosphorylation sites (Ser:56, Thr:29, Tyr:5), of which 22 were functional sites. (b) MYBL1 had 1 common methylation site and 90 common phosphorylation sites (Ser:50, Thr:33, Tyr:7), of which 21 were functional sites. (c) MYBL2 had 81 common phosphorylation sites (Ser:48, Thr:31, Tyr:2), of which 24 were functional si.

Figure 2

Structural comparison of wild-type MYB family proteins with their mutant forms. (a) 3D model of wild-type MYB protein. (b) Superimposed structures of wild-type MYB protein and its mutant having mutation from Glycine to Serine at position 111. (c) Superimposed structures of wild-type MYB protein and its mutant having mutation from Asparagine to Serine at position 183. (d) 3D model of wild-type MYBL1 protein. (e) Superimposed structures of wild-type MYBL1 protein and its mutant having mutation from Glycine to Serine at position 122. (f) 3D model of wild-type MYBL2 protein. (g) Superimposed structures of wild-type MYBL2 protein and its mutant having mutation from Serine to Cysteine at position 178.This figure was generated using UCSF Chimera 1.15 (https://www.cgl.ucsf.edu/chimera/download.html).

Figure 3

Diagrammatic representation of methodology.