Structure prediction of polyglutamine disease proteins: comparison of methods

Computational insights into missense mutations in HTT gene causing Huntington's disease and its interactome networks

BACKGROUND

Huntington's disease is a rare neurodegenerative illness of the central nervous system that is inherited in an autosomal dominant pattern. Mutant huntingtin protein is produced as a result of enlargement of CAG repeat in the N-terminal of the polyglutamine tract.

AIM OF THE STUDY

Herein, we aim to investigate the mutations and their effects on the HTT gene and its genetic variants. Additionally, the protein-protein interaction of HTT with other proteins and receptor-ligand interaction with the three-dimensional structure of huntingtin protein were identified.

METHODS

A comprehensive analysis of the HTT interactome and protein-ligand interaction has been carried out to provide a global picture of structure-function analysis of huntingtin protein. Mutations were analyzed and mutation verification tools were used to check the effect of mutation on protein function.

RESULTS

The results showed, mutations in a single gene are not only responsible for causing a particular disease but may also cause other hereditary disorders as well. Moreover, the modification at the nucleotide level also cause the change in the specific amino acid which may disrupt the function of HTT and its interacting proteins contributing in disease pathogenesis. Furthermore, the interaction between MECP2 and BDNF lowers the rate of transcriptional activity. Molecular docking further confirmed the strong interaction between MECP2 and BDNF with highest affinity. Amino acid residues of the HTT protein, involved in the interaction with tetrabenazine were N912, Y890, G2385, and V2320. These findings proved, tetrabenazine as one of the potential therapeutic agent for treatment of Huntington's disease.

CONCLUSION

These results give further insights into the genetics of Huntington's disease for a better understanding of disease models which will be beneficial for the future therapeutic studies.

Structure analysis of the proteins associated with polyA repeat expansion disorders

Repeat regions are low-complexity regions in the human genome that largely code for intrinsic disorder in proteins. Expansions outside the normal thresholds in repeat regions are likely to be pathogenic, leading to the so-called repeat expansion diseases. There have been numerous studies on the most common group of repeat expansion diseases, which are the polyglutamine (polyQ) repeat expansion diseases, but there has been much less work done on the second-largest group of expansion repeats disorders, which involves the expansion of polyalanine (polyA) repeat tracts. In this article, we present a comprehensive study of the structural changes predicted using I-TASSER when comparing the wild type and enlarged structures of all known polyA expansion disorders. The results show that there is a reduction in α helices, an increase in extended strands in parallel and/or anti-parallel β-sheet conformation, an increase in random coils/loops and irregular elements, and a large increase in solvent-accessible surface area. When compared to the findings in polyQ expansions disorders we see similar trends, suggesting that the polyQ and polyA repeat expansion causes similar effects on the respective proteins, which lead to higher misfolding and aggregation propensities.Communicated by Ramaswamy H. Sarma.

Understanding protein structural changes for oncogenic missense variants

Understanding and predicting the changes of protein structure and function upon mutation and their relationship to human health is a critical element to translate the genomic revolution into actionable interventions. Therefore, it is pertinent to explore how mutations result in structural changes leading to pathogenic proteins, but due to the protein structural knowledge gap, experimental approaches are lacking. Protein structure prediction methods, such as I-TASSER, have made it possible to predict the structure of a given amino acid sequence, thus opening a new way to explore protein structure changes upon mutations when experimental information is not available. Using known mutations from the Catalogue of Somatic Mutation in Cancer (COSMIC) and ClinVar databases, we compare predicted structure-derived properties from wild type (WT) and mutated proteins and find differences between the local and global 3D protein structures of the WT and the mutants. The studies in this relatively small sample reveal that the structural changes are quite diverse.

Effects of the enlargement of polyglutamine segments on the structure and folding of ataxin-2 and ataxin-3 proteins

Spinocerebellar ataxia type 2 (SCA2) and type 3 (SCA3) are two common autosomal-dominant inherited ataxia syndromes, both of which are related to the unstable expansion of trinucleotide CAG repeats in the coding region of the related ATXN2 and ATXN3 genes, respectively. The poly-glutamine (poly-Q) tract encoded by the CAG repeats has long been recognized as an important factor in disease pathogenesis and progress. In this study, using the I-TASSER method for 3D structure prediction, we investigated the effect of poly-Q tract enlargement on the structure and folding of ataxin-2 and ataxin-3 proteins. Our results show good agreement with the known experimental structures of the Josephin and UIM domains providing credence to the simulation results presented here, which show that the enlargement of the poly-Q region not only affects the local structure of these regions but also affects the structures of functional domains as well as the whole protein. The changes observed in the predicted models of the UIM domains in ataxin-3 when the poly-Q track is enlarged provide new insights on possible pathogenic mechanisms.