Relationships of mRNA-protein secondary structures in the human β-globin gene HBB and four variants

Abstract

Single nucleotide polymorphism is an interesting problem that can alter gene expression, recode amino acids and affect protein function. Protein structural changes have generally been attributed to amino acid replacements, and only a few research efforts have examined the effects of mRNA structural changes to the conformation of the corresponding protein coded by the mRNA. In the present study, the human β-globin HBB gene and four variants were examined. The mRNA secondary structures were constructed using the dynamic extended folding method and the encoded protein secondary structures were obtained from related databases. Comparisons were performed between these structures before and after mutations were introduced into the mature mRNAs and the proteins. We focused on the structural changes from mRNA to protein and found that regular protein conformations tend to match stable mRNA regions, whereas irregular protein conformations, such as β/γ turns and random coils, often match unstable mRNA regions. Mutations within unstable regions can alter the mRNA secondary structure and leave footprints in the protein structure. Comparison of the mRNA-protein secondary structure relationships represents a potential strategy to explore protein functional changes. © 2012 The Author(s).