Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, Shandong Province, People's Republic of China.
J Mol Model. 2012 Feb;18(2):791-802. doi: 10.1007/s00894-011-1101-9. Epub 2011 May 20.
In order to simulate the hydrogen bonding and proton transfer (PT) in protein-DNA/RNA interactions, a series of simplified models were employed and investigated in the gas phase. These models included various neutral, anionic and cationic glycine-uracil dimers, and their methylated derivatives generated by the mono- or dimethylation of glycine and/or uracil moieties of the dimer. The results reveal that the only process that can occur in the neutral complexes is a double-PT process leading to proton exchange between the two moieties (i.e., point mutation). The first methyl substitute can reduce the activation energy of the PT process and thus promote the isomerization of the two moieties; further methylation can reduce the isomerization in only some of the cases. In the anionic complexes, only the one-way PT (i.e., amino acid → nucleic acid base) process is energetically favorable, and this PT process is an interesting barrier-free one (BFPT), with the attached electron locating itself at the base moiety. Methylation will disfavor BFPT, but it cannot alter the nature of BFPT. In the cationic complexes, three different PT processes can occur. These processes can transform mutually by adjusting either or both of the methylated sites and methyl number, indicating that the methylation can regulate the dynamics of these PT processes.
为了模拟蛋白质-DNA/RNA 相互作用中的氢键和质子转移（PT），在气相中采用了一系列简化模型进行了研究。这些模型包括各种中性、阴离子和阳离子甘氨酸-尿嘧啶二聚体，以及通过二聚体的甘氨酸和/或尿嘧啶部分的单甲基化或二甲基化生成的它们的甲基化衍生物。结果表明，中性复合物中唯一能发生的过程是双 PT 过程，导致两个部分之间的质子交换（即点突变）。第一个取代甲基可以降低 PT 过程的活化能，从而促进两个部分的异构化；进一步的甲基化在某些情况下只能降低异构化。在阴离子复合物中，只有单方向的 PT（即氨基酸→核酸碱基）过程在能量上是有利的，并且这个 PT 过程是一个有趣的无势垒（BFPT）过程，所附着的电子位于碱基部分。甲基化会不利于 BFPT，但不能改变 BFPT 的性质。在阳离子复合物中，有三个不同的 PT 过程可以发生。这些过程可以通过调整一个或两个甲基化位点和甲基化数来相互转化，表明甲基化可以调节这些 PT 过程的动力学。
