THE ENERGETIC BASIS OF SPECIFICITY IN THE ECO RI ENDONUCLEASE DNA INTERACTION
THE ENERGETIC BASIS OF SPECIFICITY IN THE ECO RI ENDONUCLEASE DNA INTERACTION
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DOI：
10.1126/science.2237428
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发表时间：
1990-11-09
期刊：
影响因子：
56.9
通讯作者：
JENJACOBSON, L
中科院分区：
文献类型：
--
作者：
LESSER, DR;KURPIEWSKI, MR;JENJACOBSON, L
通过测定Eco RI核酸内切酶对识别位点GAATTC和系统改变的DNA位点的区分，分析了DNA-蛋白相互作用的高序列选择性。保留序列依赖构象基序GAATTC位点的碱基类似取代允许以+1至+2 kcal/mol的代价删除蛋白质-碱基接触的单个位点。然而，任何一个不正确的天然碱基对的引入都要耗费+6到+13 kcal/mol的过渡态相互作用能，这是以下相互依赖因素的结果：蛋白质和嘌呤碱基之间的一个或两个氢键的缺失；在蛋白质上的基团和在碱基上不正确放置的官能团之间不利的空间排列；破坏与蛋白质的嘧啶接触；DNA磷酸盐之间的一些关键相互作用丧失；以及在过渡态复合体中获得所需DNA构象的能量成本增加。因此，Eco RI内切酶通过DNA序列的“直接读出”（蛋白质碱基接触）和“间接读出”（蛋白质-磷酸盐接触和DNA构象）实现严格的识别。
High sequence selectivity in DNA-protein interactions was analyzed by measuring discrimination by Eco RI endonuclease between the recognition site GAATTC and systematically altered DNA sites. Base analogue substitutions that preserve the sequence-dependent conformational motif GAATTC site permit deletion of single sites of protein-base contact at a cost of +1 to +2 kcal/mol. However, the introduction of any one incorrect natural base pair costs +6 to +13 kcal/mol in transition state interaction energy, the resultant of the following interdependent factors: deletion of one or two hydrogen bonds between the protein and a purine base; unfavorable steric apposition between a group on the protein and an incorrectly placed functional group on a base; disruption of a pyrimidine contact with the protein; loss of some crucial interactions between and DNA phosphates; and an increased energetic cost of attaining the required DNA conformation in the transition state complex. Eco RI endonuclease thus achieves stringent discrimination by both "direct readout" (protein-base contacts) and "indirect readout" (protein-phosphate contacts and DNA conformation) of the DNA sequence.