Prediction of binding modes between protein L-isoaspartyl (D-aspartyl) O-methyltransferase and peptide substrates including isomerized aspartic acid residues using in silico analytic methods for the substrate screening.

Because the aspartic acid (Asp) residues in proteins are occasionally isomerized in the human body, not only l-α-Asp but also l-ß-Asp, D-α-Asp and D-ß-Asp are found in human proteins. In these isomerized aspartic acids, the proportion of D-ß-Asp is the largest and the proportions of l-ß-Asp and D-α-Asp found in human proteins are comparatively small. To explain the proportions of aspartic acid isomers, the possibility of an enzyme able to repair l-ß-Asp and D-α-Asp is frequently considered. The protein L-isoaspartyl (D-aspartyl) O-methyltransferase (PIMT) is considered one of the possible repair enzymes for l-ß-Asp and D-α-Asp. Human PIMT is an enzyme that recognizes both l-ß-Asp and D-α-Asp, and catalyzes the methylation of their side chains. In this study, the binding modes between PIMT and peptide substrates containing l-ß-Asp or D-α-Asp residues were investigated using computational protein-ligand docking and molecular dynamics simulations. The results indicate that carboxyl groups of both l-ß-Asp and D-α-Asp were recognized in similar modes by PIMT and that the C-terminal regions of substrate peptides were located in similar positions on PIMT for both the l-ß-Asp and D-α-Asp peptides. In contrast, for peptides containing l-α-Asp or D-ß-Asp residues, which are not substrates of PIMT, the computationally constructed binding modes between PIMT and peptides greatly differed from those between PIMT and substrates. In the nonsubstrate peptides, not inter- but intra-molecular hydrogen bonds were observed, and the conformations of peptides were more rigid than those of substrates. Thus, the in silico analytical methods were able to distinguish substrates from nonsubstrates and the computational methods are expected to complement experimental analytical methods.

Computational investigation of the substrate recognition mechanism of protein D-aspartyl (L-isoaspartyl) O-methyltransferase by docking and molecular dynamics simulation studies and application to interpret size exclusion chromatography data.

Unusual amino acid residues such as L-ß-aspartyl (Asp), D-α-Asp, and D-ß-Asp have been detected in proteins and peptides such as α-crystallin in the lens and ß-amyloid in the brain. These residues increase with age, and hence they are associated with age-related diseases. The enzyme protein D-aspartyl (L-isoaspartyl) O-methyltransferase (PIMT) can revert these residues back to the normal L-α-Asp residue. PIMT catalyzes transmethylation of S-adenosylmethionine to L-ß-Asp and D-α-Asp residues in proteins and peptides. In this work, the substrate recognition mechanism of PIMT was investigated using docking and molecular dynamics simulation studies. It was shown that the hydrogen bonds of Ser60 and Val214 to the carboxyl group of Asp are important components during substrate recognition by PIMT. In addition, specific hydrogen bonds were observed between the main chains of the substrates and those of Ala61 and Ile212 of PIMT when PIMT recognized L-ß-Asp. Hydrophobic interactions between the (n-1) residue of the substrates and Ile212 and Val214 of PIMT may also have an important effect on substrate binding. Volume changes upon substrate binding were also evaluated in the context of possible application to interpretation of size exclusion chromatography data.