Wild-Type RNA MicrohelixAla and 3:70 Variants: Molecular Dynamics Analysis of Local Helical Structure and Tightly Bound Water
Wild-Type RNA MicrohelixAla and 3:70 Variants: Molecular Dynamics Analysis of Local Helical Structure and Tightly Bound Water
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野生型 RNA MicrohelixAla 和 3:70 变体：局部螺旋结构和紧密结合水的分子动力学分析
DOI：
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发表时间：
1999
期刊：
影响因子：
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通讯作者：
C. Cramer
中科院分区：
文献类型：
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作者：
Maria C. Nagan;Stephanie S. Kerimo;K. Musier;C. Cramer
RNA微螺旋Ala的分子动力学模拟表明，G：U和其他3：70嘌呤：嘧啶摆动对在其各自的微螺旋中诱导局部偏离A型几何形状;螺旋在碱基对步骤上方欠缠绕，在碱基对步骤下方过度缠绕，在每种情况下与典型的A型RNA相比约为7-9°。平均水密度和停留寿命的分析的基础上，野生型微螺旋强烈结合在小沟的3：70碱基对的水分子，与来自大肠杆菌tRNA Ala的受体茎的RNA双链体的晶体学分析一致。其他摆动对在这个位置显示水结合，但程度较低;水结合的强度与作为E.大肠杆菌丙氨酰-tRNA合成酶（G：U > 2AA：IsoC > G：dU > I：U）。在3：70位置的沃森-克里克碱基对没有显示出特定水合作用的趋势。这种紧密结合的小沟水在微螺旋与3：70摆动对显然不起作用，以稳定一个特定的局部螺旋结构，但它可能发挥作用，作为一个特定的识别元件或作为一个指标之间的相互作用的特异性微螺旋和氨酰-tRNA合成酶的氢键残基。
Molecular dynamics simulations of RNA microhelix Ala indicate that G:U and other 3:70 purine: pyrimidine wobble pairs induce local deviations from A-form geometry in their respective microhelices; the helix is underwound at the base-pair step above and overwound at the base-pair step below, in each case by about 7-9° compared to canonical A-form RNA. On the basis of analysis of average water densities and residence lifetimes, the wild-type microhelix strongly binds a water molecule in the minor groove of the 3:70 base pair, consistent with crystallographic analyses of an RNA duplex derived from the acceptor stem of Escherichia coli tRNA Ala . Other wobble pairs show water binding at this position but to a lesser degree; the strength of water binding correlates directly with the measured aminoacylation activities of the microhelices as substrates for E. coli alanyl-tRNA synthetase (G:U > 2AA:IsoC > G:dU > I:U). Watson-Crick base pairs at the 3:70 position show no tendency toward specific hydration. This tightly bound minor-groove water in the microhelices with 3:70 wobble pairs evidently does not function to stabilize a particular local helical structure, but it may play a role as a specific recognition element or serve as an indicator of interaction specificity between the microhelix and a hydrogen-bonding residue of the aminoacyl-tRNA synthetase.