Cooperativity in drug-DNA recognition: A molecular dynamics study

被引:136
作者
Harris, SA
Gavathiotis, E
Searle, MS
Orozco, M
Laughton, CA
机构
[1] Sch Pharmaceut Sci, Nottingham NG7 2RD, England
[2] Sch Chem, Nottingham NG7 2RD, England
[3] Univ Barcelona, Fac Quim, Dept Bioquim, E-08028 Barcelona, Spain
关键词
D O I
10.1021/ja016233n
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
NMR studies have shown that the minor groove-binding ligand Hoechst 33258 binds to the two T-4/A(4) tracts within the duplex d(CTTTTCGAAAAG)(2) in a highly cooperative manner, such that in titration experiments no intermediate 1:1 complex can be detected. The NMR-derived structures of the free DNA and the 2:1 complex have been obtained, but can shed little light on what the origins of this cooperativity may be. Here we present the results of a series of molecular dynamics simulations on the free DNA, the 1: 1 complex, and the 2:1 complex, which have been designed to enable us to calculate thermodynamic parameters associated with the molecular recognition events. The results of the molecular dynamics studies confirm that structural factors alone cannot explain the cooperativity observed, indeed when enthalpic and hydration factors are looked at in isolation, the recognition process is predicted to be slightly anticooperative. However, when change,,; in configurational entropy are taken into account as well, the overall free energy differences are such that the calculated cooperativity is in good agreement with that observed experimentally. The results indicate the power of molecular dynamics methods to provide reasonable explanations for phenomena that are difficult to explain on the basis of static models alone, and provide a nice example of the concept of "allostery without conformational change".
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页码:12658 / 12663
页数:6
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