Ramachandran Srinivas, Temple Brenda R, Chaney Stephen G, Dokholyan Nikolay V
Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-7260, USA.
Nucleic Acids Res. 2009 May;37(8):2434-48. doi: 10.1093/nar/gkp029. Epub 2009 Mar 2.
The differences in efficacy and molecular mechanisms of platinum based anti-cancer drugs cisplatin (CP) and oxaliplatin (OX) have been hypothesized to be in part due to the differential binding affinity of cellular and damage recognition proteins to CP and OX adducts formed on adjacent guanines in genomic DNA. HMGB1a in particular exhibits higher binding affinity to CP-GG adducts, and the extent of discrimination between CP- and OX-GG adducts is dependent on the bases flanking the adducts. However, the structural basis for this differential binding is not known. Here, we show that the conformational dynamics of CP- and OX-GG adducts are distinct and depend on the sequence context of the adduct. Molecular dynamics simulations of the Pt-GG adducts in the TGGA sequence context revealed that even though the major conformations of CP- and OX-GG adducts were similar, the minor conformations were distinct. Using the pattern of hydrogen bond formation between the Pt-ammines and the adjacent DNA bases, we identified the major and minor conformations sampled by Pt-DNA. We found that the minor conformations sampled exclusively by the CP-GG adduct exhibit structural properties that favor binding by HMGB1a, which may explain its higher binding affinity to CP-GG adducts, while these conformations are not sampled by OX-GG adducts because of the constraints imposed by its cyclohexane ring, which may explain the negligible binding affinity of HMGB1a for OX-GG adducts in the TGGA sequence context. Based on these results, we postulate that the constraints imposed by the cyclohexane ring of OX affect the DNA conformations explored by OX-GG adduct compared to those of CP-GG adduct, which may influence the binding affinities of HMG-domain proteins for Pt-GG adducts, and that these conformations are further influenced by the DNA sequence context of the Pt-GG adduct.
顺铂（CP）和奥沙利铂（OX）这两种铂类抗癌药物在疗效和分子机制上的差异，据推测部分是由于细胞和损伤识别蛋白对基因组DNA中相邻鸟嘌呤上形成的CP和OX加合物的结合亲和力不同。特别是高迁移率族蛋白B1a（HMGB1a）对CP-GG加合物表现出更高的结合亲和力，并且CP-和OX-GG加合物之间的区分程度取决于加合物两侧的碱基。然而，这种差异结合的结构基础尚不清楚。在此，我们表明CP-和OX-GG加合物的构象动力学是不同的，并且取决于加合物的序列背景。在TGGA序列背景下对Pt-GG加合物进行的分子动力学模拟表明，尽管CP-和OX-GG加合物的主要构象相似，但次要构象是不同的。利用铂胺与相邻DNA碱基之间形成氢键的模式，我们确定了Pt-DNA采样的主要和次要构象。我们发现，仅由CP-GG加合物采样的次要构象具有有利于HMGB1a结合的结构特性，这可能解释了其对CP-GG加合物具有更高的结合亲和力，而OX-GG加合物由于其环己烷环施加的限制而不采样这些构象，这可能解释了在TGGA序列背景下HMGB1a对OX-GG加合物的结合亲和力可忽略不计。基于这些结果，我们推测与CP-GG加合物相比，OX的环己烷环施加的限制会影响OX-GG加合物所探索的DNA构象，这可能会影响HMG结构域蛋白对Pt-GG加合物的结合亲和力，并且这些构象会进一步受到Pt-GG加合物的DNA序列背景的影响。
