Structural characterization of mutant α-galactosidases causing Fabry disease

Abstract

Fabry disease is an inborn error of glycolipid catabolism resulting from lesions in the gene encoding agalactosidase (GLA). To elucidate the basis of Fabry disease, we constructed structural models of mutant GLAs responsible for the disease and calculated indexes, i.e., the numbers of atoms affected in the main chain and side chain of each mutant GLA, the root-mean-square distance values, and the solvent-accessible surface-area values, based on 212 Fabry amino acid substitutions previously reported (196 classic and 16 variant). As two therapeutic options, enzyme replacement and enzyme enhancement, are now available for this disease, proper prediction of the natural outcome and therapeutic efficiency based on the molecular evidence for individual cases are critical for patients' quality of life. Our results revealed that structural changes in the classic Fabry group were generally large and tended to be in the core region of a protein or located in the functionally important region, including the active-site pocket. On the other hand, structural changes in the variant Fabry group were small or localized on the surface of the molecule far away from the active site. We focused on structural changes due to amino acid substitutions for which substrate analogues are effective for improving the stability or transportation of mutant GLAs, and the results of the study revealed that they are small or localized on the molecular surface, regardless of the phenotype. Coloring of affected atoms based on distances between wild type and mutant ones clearly showed the characteristic structural changes in the GLA protein geographically and subquantitatively. Structural investigation is useful for elucidation of the basis of Fabry disease and predicting disease outcome.

Structural modeling of mutant α-glucosidases resulting in a processing/transport defect in Pompe disease

“…[18][19][20][21][22] We defined that the structure was influenced by an amino acid substitution when the position of an atom in a mutant differed from that in the wild-type structure by more than the cut-off distance (0.15 Å ) on the basis of the total root-mean-square distance (RMSD), as described earlier. [18][19][20][21][22] The numbers of influenced atoms in the main chain and the side chain were calculated. Abbreviations: ASA, solvent-accessible surface area; RMSD, root-mean-square distance; À, no protein; ¼, normal amount; m, more than normal; k, less than normal.…”

“…20,22,23 Determination of the solvent-accessible surface area (ASA) values of amino acid residues causing a processing/transport defect in Pompe disease…”

“…The analysis is on the basis of the geographic distances between the wild-type and substituted amino acid residues in the three-dimensional model, according the method described earlier. [19][20][21][22]25 Structural modeling of the surface region affected by representative amino acid substitutions…”

Biochemical and structural study on a S529V mutant acid α-glucosidase responsive to pharmacological chaperones

“…We defined that the structure was influenced by an amino acid substitution when the position of an atom in a mutant structure differed from that in the wild-type one by more than 0.15 Å , based on total root mean square distance, and the numbers of influenced atoms in the main chain and the side chain were calculated, as described previously. 24 Determination of root mean square distance values of all atoms in the mutant GAA structures…”

“…24 Determination of solvent-accessible surface area (ASA) values of amino-acid residues in the mutant GAA structures…”