Czyznikowska Zaneta
Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jagiellonska 13-15, 85-067 Bydgoszcz, Poland.
J Mol Model. 2009 Jun;15(6):615-22. doi: 10.1007/s00894-008-0447-0. Epub 2009 Feb 7.
This study reports on ab initio calculations of adenine-cytosine complexes in two different context alignments appearing in B-DNA. The influence of adenine modification by hydroxyl radical on the stability of the complexes is also discussed. The analysis was performed on over 40 crystallographic structures for each of the sequence contexts. In most cases, modification of adenine by hydroxyl radical leads to less negative intermolecular interaction energies. The issue of the influence of alteration of structural base step parameters on the stability of modified and unmodified adenine-cytosine complexes is also addressed. Analysis of the dependence of intermolecular interaction energy on base step parameters reveals that for twist and shift modification of adenine by hydroxyl radical leads to quite different interaction energy profiles in comparison with unmodified complexes. In order to elucidate the physical origins of this phenomenon, i.e. to analyze how the modification of adenine by hydroxyl radical is reflected in the change of intermolecular interaction energy components, a variational-perturbational decomposition scheme was applied at the MP2/aug-cc-pVDZ level of theory.
本研究报告了对B-DNA中出现的两种不同上下文比对中的腺嘌呤-胞嘧啶复合物进行的从头计算。还讨论了羟基自由基对腺嘌呤的修饰对复合物稳定性的影响。对每种序列上下文的40多个晶体结构进行了分析。在大多数情况下，羟基自由基对腺嘌呤的修饰导致分子间相互作用能的负值减小。还探讨了结构碱基步参数的改变对修饰和未修饰的腺嘌呤-胞嘧啶复合物稳定性的影响问题。分子间相互作用能对碱基步参数的依赖性分析表明，与未修饰的复合物相比，羟基自由基对腺嘌呤的扭曲和位移修饰导致了截然不同的相互作用能分布。为了阐明这一现象的物理根源，即分析羟基自由基对腺嘌呤的修饰如何反映在分子间相互作用能成分的变化中，在MP2/aug-cc-pVDZ理论水平上应用了变分微扰分解方案。
