Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4.
J Chem Theory Comput. 2008 Oct 14;4(10):1768-80. doi: 10.1021/ct8002332.
T-shaped geometries and interaction energies between select DNA nucleobases (adenine or 3-methyladenine) and all aromatic amino acids (histidine, phenylalanine, tyrosine, or tryptophan) were examined using BSSE-corrected MP2/6-31G*(0.25) potential energy surface scans, which determined the preferred nucleobase (face)-amino acid (edge) and nucleobase (edge)-amino acid (face) interactions. The energies of dimers with the strongest interactions were further studied at the CCSD(T)/CBS level of theory, which suggests that the T-shaped interactions in adenine dimers are very strong (up to -35 kJ mol(-1)). Nucleobase methylation to form a cationic damaged base (3-methyladenine) plays a large role in the relative monomer orientations and magnitude of the interactions, which increase by 17-125%. Most importantly, this study is the first to compare the stacking and T-shaped interactions between all aromatic amino acids and select (natural and damaged) DNA nucleobases where the differences between stacking and T-shaped interactions at the CCSD(T)/CBS level are small. Therefore, our results indicate that T-shaped interactions cannot be ignored when studying biological processes, and this manuscript discusses the importance of these interactions in the context of DNA repair.
采用 BSSE 校正的 MP2/6-31G*(0.25) 势能面扫描，研究了选定的 DNA 碱基（腺嘌呤或 3-甲基腺嘌呤）与所有芳香族氨基酸（组氨酸、苯丙氨酸、酪氨酸或色氨酸）之间的 T 型几何形状和相互作用能，确定了首选的碱基（面）-氨基酸（边）和碱基（边）-氨基酸（面）相互作用。在 CCSD(T)/CBS 理论水平上进一步研究了具有最强相互作用的二聚体的能量，这表明腺嘌呤二聚体中的 T 型相互作用非常强（高达-35 kJ mol(-1))。形成阳离子损伤碱基（3-甲基腺嘌呤）的碱基甲基化在相对单体取向和相互作用的大小中起着重要作用，相互作用的大小增加了 17-125%。最重要的是，这项研究首次比较了所有芳香族氨基酸和选定（天然和损伤）DNA 碱基之间的堆积和 T 型相互作用，其中 CCSD(T)/CBS 水平上堆积和 T 型相互作用之间的差异很小。因此，我们的结果表明，在研究生物过程时不能忽略 T 型相互作用，本文讨论了这些相互作用在 DNA 修复中的重要性。
