On the role of steric clashes in methylation control of restriction endonuclease activity
On the role of steric clashes in methylation control of restriction endonuclease activity
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DOI：
10.1093/nar/gkv1341
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发表时间：
2016-01-08
影响因子：
14.9
通讯作者：
Czapinska, Honorata
中科院分区：
文献类型：
--
作者：
Mierzejewska, Karolina;Bochtler, Matthias;Czapinska, Honorata
限制修饰系统消化非甲基化的入侵DNA，同时通过甲基化保护宿主DNA免受内切酶活性的影响。人们普遍认为，甲基化的DNA在生产方向上不会“适合”进入核酸内切酶的结合位点，因此空间冲突应该是大部分保护的原因。我们测试这一概念的统计接枝甲基基团在硅上的非甲基化DNA的共晶体结构与限制性内切核酸酶。保护性甲基化的冲突得分显著高于非保护性甲基化（根据Wilcoxon秩和检验，P < 0.05%）。仅结构数据就足以区分保护性和非保护性DNA甲基化，90%的置信度和决策阈值分别为1.1埃和48埃（3），用于与蛋白质最严重的基于距离和基于累积体积的冲突（从每个原子间距离中扣除0.1埃以允许坐标误差）。最严重的冲突是更明显的保护甲基连接到氮原子（N6-甲基腺嘌呤和N4-甲基胞嘧啶）比胞嘧啶上的C5-甲基。对于所有三种类型的保护性甲基化，累积冲突是相当的。
Restriction-modification systems digest non-methylated invading DNA, while protecting host DNA against the endonuclease activity by methylation. It is widely believed that the methylated DNA would not 'fit' into the binding site of the endonuclease in the productive orientation, and thus steric clashes should account for most of the protection. We test this concept statistically by grafting methyl groups in silico onto non-methylated DNA in co-crystal structures with restriction endonucleases. Clash scores are significantly higher for protective than non-protective methylation (P < 0.05% according to the Wilcoxon rank sum test). Structural data alone are sufficient to distinguish between protective and non-protective DNA methylation with 90% confidence and decision thresholds of 1.1 angstrom and 48 angstrom(3) for the most severe distance-based and cumulative volume-based clash with the protein, respectively (0.1 angstrom was deducted from each interatomic distance to allow for coordinate errors). The most severe clashes are more pronounced for protective methyl groups attached to the nitrogen atoms (N6-methyladenines and N4-methylcytosines) than for C5-methyl groups on cytosines. Cumulative clashes are comparable for all three types of protective methylation.