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Structural variation induced by different nucleotides at the cleavage site of the hammerhead ribozyme

机译：锤头状核酶裂解位点上不同核苷酸诱导的结构变异

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摘要

The hammerhead ribozyme is capable of cleaving RNA substrates at 5' UX 3' sequences (where the cleavage site, X, can be A, C, or U). Hammerhead complexes containing dC, dA, dI, or rG nucleotides at the cleavage site have been studied by NMR. The rG at the cleavage site forms a Watson-Crick base pair with C3 in the conserved core of the hammerhead, indicating that rG substrates inhibit the cleavage reaction by stabilizing an inactive conformation of the molecule. isotope-edited NMR experiments on the hammerhead complexes show that there are different short proton-proton distances between neighboring residues depending upon whether there is a dC or dA at the cleavage site. These NMR data demonstrate that there are significant differences in the structure and/or dynamics of the active-site residues in these hammerhead complexes, Molecular dynamics calculations were used to model the conformations of the cleavage-site variants consistent with the NMR data. The solution conformations of the hammerhead ribozyme-substrate complexes are compared with the X-ray structure of the hammerhead ribozyme and are used to help understand the thermodynamic and kinetic differences among the cleavage-site variants. [References: 40]
机译：锤头状核酶能够切割5'UX 3'序列（其中切割位点X可以是A，C或U）的RNA底物。通过NMR研究了在切割位点含有dC，dA，dI或rG核苷酸的锤头复合体。裂解位点处的rG与锤头的保守核中的C3形成沃森-克里克碱基对，表明rG底物通过稳定分子的非活性构象来抑制裂解反应。锤头配合物的同位素编辑NMR实验表明，取决于在裂解位点处存在dC或dA，相邻残基之间存在不同的短质子-质子距离。这些NMR数据表明在这些锤头配合物中活性位点残基的结构和/或动力学上存在显着差异。使用分子动力学计算来模拟与NMR数据一致的切割位点变体的构象。将锤头型核酶-底物复合物的溶液构型与锤头型核酶的X射线结构进行比较，并用于帮助理解裂解位点变体之间的热力学和动力学差异。 [参考：40]

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