A computational method to characterize the missense mutations in the catalytic domain of GAA protein causing Pompe disease

Abstract

Pompe disease is an autosomal recessive lysosomal storage disease caused by acid α-glucosidase (GAA) deficiency, resulting in intralysosomal accumulation of glycogen, including cardiac, skeletal, and smooth muscle cells. The GAA gene is located on chromosome 17 (17q25.3), the GAA protein consists of 952 amino acids; of which 378 amino acids (347-726) falls within the catalytic domain of the protein and comprises of active sites (518 and 521) and binding sites (404, 600, 616, and 674). In this study, we used several computational tools to classify the missense mutations in the catalytic domain of GAA for their pathogenicity and stability. Eight missense mutations (R437C, G478R, N573H, Y575S, G605D, V642D, L705P, and L712P) were predicted to be pathogenic and destabilizing to the protein structure. These mutations were further subjected to phenotyping analysis using SNPeffect 4.0 to predict the chaperone binding sites and structural stability of the protein. The mutations R437C and G478R were found to compromise the chaperone-binding activity with GAA. Molecular docking analysis revealed that the G478R mutation to be more significant and hinders binding to the DNJ (Miglustat) compared with the R437C. Further molecular dynamic analysis for the two mutations demonstrated that the G478R mutation was acquired higher deviation, fluctuation, and lower compactness with decreased intramolecular hydrogen bonds compared to the mutant R437C. These data are expected to serve as a platform for drug design against Pompe disease and will serve as an ultimate tool for variant classification and interpretations.

The impact of missense mutation in PIGA associated to paroxysmal nocturnal hemoglobinuria and multiple congenital anomalies-hypotonia-seizures syndrome 2: A computational study

“…Molecular dynamics (MD) simulation technique has been progressively utilized to reveal the impact of mutations over the stability of protein structure at atomistic level and the role of each residue in the native as well as in the mutant structures (Thirumal Kumar et al. 2019a, 2019b). Hence, to have the more detailed insight on the effect of mutations over the structure and dynamics of the protein, MD simulation of native wild type and the four pathogenic mutants (screened by series of in-silico tools) were performed.…”

Molecular insights into the coding region mutations of low‐density lipoprotein receptor adaptor protein 1 (LDLRAP1) linked to familial hypercholesterolemia

“…In the present study, we selected the prediction scores of four different methods, including Polymorphism Phenotyping (PolyPhen) (http://genetics.bwh.harvard.edu/pph2/), Scale‐invariant Feature Transform (SIFT), Mendelian Clinically Applicable Pathogenicity (M‐CAP) and Combined Annotation Dependent Depletion (CADD) (https://www.cadd.gs.washington.edu). The consequences of these variants on the transcript were described in accordance with the guidance on Sequence Ontology terms …”

Induced pluripotent stem cell for modeling Pompe disease

“…Point mutations can influence posttranscriptional splicing or directly change the GAA protein function, while deletions and/or insertions of DNA fragments may yield unstable mRNA transcription, thus finally affecting protein translation, posttranslational modifications, trafficking into the lysosome, and glycogenolysis activity of GAA. As the most reported mutation type, missense mutations of the GAA gene occurring in the unexposed amino acid residues often result in misfolding of the 3D protein structure ( 19 , 20 ).…”