Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Sendai, Miyagi 981-8558, Japan.
J Chromatogr B Analyt Technol Biomed Life Sci. 2011 Nov 1;879(29):3310-6. doi: 10.1016/j.jchromb.2011.06.021. Epub 2011 Jun 21.
Unusual amino acid residues such as L-β-aspartyl (Asp), D-α-Asp, and D-β-Asp have been detected in proteins and peptides such as α-crystallin in the lens and β-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-β-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-β-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.
已在晶状体中的 α- 晶体蛋白和大脑中的 β- 淀粉样蛋白等蛋白质和肽中检测到不常见的氨基酸残基，如 L-β-天冬氨酸（Asp）、D-α-Asp 和 D-β-Asp。这些残基随年龄增加而增加，因此与年龄相关的疾病有关。酶蛋白 D-天冬氨酸（L-异天冬氨酸）O- 甲基转移酶（PIMT）可以将这些残基恢复为正常的 L-α-Asp 残基。PIMT 催化 S-腺苷甲硫氨酸向蛋白质和肽中的 L-β-Asp 和 D-α-Asp 残基的转甲基化。在这项工作中，使用对接和分子动力学模拟研究研究了 PIMT 的底物识别机制。结果表明，在 PIMT 识别底物时，Ser60 和 Val214 与 Asp 羧基的氢键是底物识别的重要组成部分。此外，当 PIMT 识别 L-β-Asp 时，观察到底物的主链与 PIMT 的 Ala61 和 Ile212 的主链之间存在特定的氢键。底物的（n-1）残基与 PIMT 的 Ile212 和 Val214 之间的疏水相互作用也可能对底物结合有重要影响。还评估了底物结合时的体积变化，以便可能用于解释尺寸排阻色谱数据。
