Structural Characterization of the Interaction of Hypoxia Inducible Factor-1 with Its Hypoxia Responsive Element at the -964G > A Variation Site of the HLA-G Promoter Region

Computational and atomistic studies applied to the understanding of the structural and behavioral features of the immune checkpoint HLA-G molecule and gene

We took advantage of the increasingly evolving approaches for in silico studies concerning protein structures, protein molecular dynamics (MD), protein-protein and protein-DNA docking to evaluate: (i) the structure and MD characteristics of the HLA-G well-recognized isoforms, (ii) the impact of missense mutations at HLA-G receptor genes (LILRB1/2), and (iii) the differential binding of the hypoxia-inducible factor 1 (HIF1) to hypoxia-responsive elements (HRE) at the HLA-G gene. Besides reviewing these topics, they were revisited including the following novel results: (i) the HLA-G6 isoforms were unstable docked or not with β₂-microglobulin or peptide, (ii) missense mutations at LILRB1/2 genes, exchanging amino acids at the intracellular domain, particularly those located within and around the ITIM motifs, may impact the HLA-G binding strength, and (iii) HREs motifs at the HLA-G promoter or exon 2 regions exhibiting a guanine at their third position present a higher affinity for HIF1 when compared to an adenine at the same position. These data shed some light into the functional aspects of HLA-G, particularly how polymorphisms may influence the role of the molecule. Computational and atomistic studies have provided alternative tools for experimental physical methodologies, which are time-consuming, expensive, demanding large quantities of purified proteins, and exhibit low output.

A computational study to assess the polymorphic landscape of matrix metalloproteinase 3 promoter and its effects on transcriptional activity

BACKGROUND

Matrix metalloproteinase 3 (MMP3) plays a crucial role in cancer progression and development by proteolyzing extracellular matrix substrates. Primarily, the expression of MMP3 is regulated at the transcriptional level. The minute interplay of various transcription factor binding motifs at the promoter region is responsible for the altered expression of the genes. Single nucleotide polymorphism (SNP) at the transcription factor binding sites shows specific effects on gene expressions. Genome-wide association study (GWAS) strongly reported the association of common SNPs (rs3025058, rs522616, and rs617819) of MMP3 promoter with disease progression. The insufficient functional analysis of these promoter SNPs indicates the need for extensive mechanistic analysis on the effects of allelic variants upon transcription factor binding at MMP3 promoter.

METHODS

The binding of transcription factors on the MMP3 promoter sequence was investigated by a virtual laboratory. The interaction between the specific transcription factor and promoter DNA with allelic variants was analyzed by computational tools.

RESULTS

It was found that transcription factor c-Myb and Smad4 binding on MMP3 promoter were altered due to the presence of rs522616 and rs617819 SNPs, respectively. Further, the binding affinity of Smad4 to the MMP3 promoter containing C allele at -375 region is higher than that of its allelic variant G.

CONCLUSION

This study presented that the complex of Smad4-DNA fragment containing C allele has higher binding affinity and stability as compared with its allelic variant. Hence, it is predicted that rs617819 polymorphism directly affects the Smad4 binding motif on MMP3 promoter and alters its gene expression.