Yan Shixiang, Wu Min, Buterin Tonko, Naegeli Hanspeter, Geacintov Nicholas E, Broyde Suse
Department of Chemistry, New York University, New York, New York 10003, USA.
Biochemistry. 2003 Mar 4;42(8):2339-54. doi: 10.1021/bi0270081.
We investigate the influence of base sequence context on the conformations of the 10S (+)- and 10R (-)-trans-anti-[BP]-N(6)-dA adducts through molecular dynamics (MD) simulations with free energy calculations, and relate the structural findings to results of nucleotide excision repair (NER) assays in human cell extracts. In previous studies, these adducts were studied in the CAA sequence context, and here we report results for the CAC sequence. Our simulations indicate that the base sequence context affects the syn-anti conformational equilibrium in the 10S (+) adduct by modulating the barrier heights between these states on the energy surface, with a higher barrier in the CAC case. Our nucleotide excision repair assay finds greater NER susceptibilities in the 10S (+) adduct for the CAC sequence context. A structural rationale ties together these results. A sequence specific hydrogen bond, accompanied by a significantly increased roll and consequent bending in the 10S (+) adduct, has been found in our simulations for the CA*C sequence, which could account for the enhanced nucleotide excision repair as well as the syn-anti equilibrium difference we observe in this isomer and sequence. Such sequence specific differential repair could contribute to the existence of mutational hotspots and thereby contribute to the complexity of cancer initiation.
我们通过结合自由能计算的分子动力学（MD）模拟，研究碱基序列背景对10S（+）-和10R（-）-反式-反式-[BP]-N（6）-dA加合物构象的影响，并将结构研究结果与人类细胞提取物中的核苷酸切除修复（NER）试验结果相关联。在先前的研究中，这些加合物是在CAA序列背景下进行研究的，而在此我们报告CAC序列的结果。我们的模拟表明，碱基序列背景通过调节能量表面上这些状态之间的势垒高度，影响10S（+）加合物中的顺-反构象平衡，在CAC情况下势垒更高。我们的核苷酸切除修复试验发现，在CAC序列背景下，10S（+）加合物的NER敏感性更高。一个结构上的原理将这些结果联系在一起。在我们对CA*C序列的模拟中发现了一个序列特异性氢键，伴随着10S（+）加合物中显著增加的滚动和随之而来的弯曲，这可以解释观察到的该异构体和序列中增强的核苷酸切除修复以及顺-反平衡差异。这种序列特异性差异修复可能导致突变热点的存在，从而导致癌症起始的复杂性。
