Bahar I, Jernigan R L
Laboratory of Experimental and Computational Biology, National Institutes of Health, Bethesda, MD 20892-5677, USA.
J Mol Biol. 1998 Sep 4;281(5):871-84. doi: 10.1006/jmbi.1998.1978.
The vibrational dynamics of transfer RNAs, both free, and complexed with the cognate synthetase, are analyzed using a model (Gaussian network model) which recently proved to satisfactorily describe the collective motions of folded proteins. The approach is similar to a normal mode analysis, with the major simplification that no residue specificity is taken into consideration, which permits us (i) to cast the problem into an analytical form applicable to biomolecular systems including about 10(3 )residues, and (ii) to acquire information on the essential dynamics of such large systems within computational times at least two orders of magnitude shorter than conventional simulations. On a local scale, the fluctuations calculated for yeast tRNAPhe and tRNAAsp in the free state, and for tRNAGln complexed with glutaminyl-tRNA synthetase (GlnRS) are in good agreement with the corresponding crystallographic B factors. On a global scale, a hinge-bending region comprising nucleotides U8 to C12 in the D arm, G20 to G22 in the D loop, and m7G46 to C48 in the variable loop (for tRNAPhe), is identified in the free tRNA, conforming with previous observations. The two regions subject to the largest amplitude anticorrelated fluctuations in the free form, i.e. the anticodon region and the acceptor arm are, at the same time, the regions that experience the most severe suppression in their flexibilities upon binding to synthetase, suggesting that their sampling of the conformational space facilitates their recognition by the synthetase. Likewise, examination of the global mode of motion of GlnRS in the complex indicates that residues 40 to 45, 260 to 270, 306 to 314, 320 to 327 and 478 to 485, all of which cluster near the ATP binding site, form a hinge-bending region controlling the cooperative motion, and thereby the catalytic function, of the enzyme. The distal beta-barrel and the tRNA acceptor binding domain, on the other hand, are distinguished by their high mobilities in the global modes of motion, a feature typical of recognition sites, also observed for other proteins. Most of the conserved bases and residues of tRNA and GlnRS are severely constrained in the global motions of the molecules, suggesting their having a role in stabilizing and modulating the global motion.
利用一种模型（高斯网络模型）分析了游离的以及与同源合成酶复合的转运RNA的振动动力学，该模型最近被证明能够令人满意地描述折叠蛋白的集体运动。这种方法类似于一种简正模式分析，主要的简化之处在于不考虑残基特异性，这使我们能够（i）将问题转化为适用于包含约10³个残基的生物分子系统的解析形式，并且（ii）在比传统模拟至少短两个数量级的计算时间内获取有关此类大型系统基本动力学的信息。在局部尺度上，计算得到的游离状态下酵母苯丙氨酸tRNA和天冬氨酸tRNA以及与谷氨酰胺 - tRNA合成酶（GlnRS）复合的谷氨酰胺tRNA的波动与相应的晶体学B因子高度吻合。在全局尺度上，在游离tRNA中确定了一个铰链弯曲区域，该区域包括D臂中的核苷酸U8至C12、D环中的G20至G22以及可变环中的m⁷G46至C48（对于苯丙氨酸tRNA），这与先前的观察结果一致。在游离形式中经历最大幅度反相关波动的两个区域，即反密码子区域和受体臂，同时也是在与合成酶结合时其灵活性受到最严重抑制的区域，这表明它们对构象空间的采样有助于合成酶对它们的识别。同样，对复合物中GlnRS全局运动模式的研究表明，位于ATP结合位点附近的残基40至45、260至270、306至314、320至327和478至485形成了一个控制酶的协同运动进而控制其催化功能的铰链弯曲区域。另一方面，远端β桶和tRNA受体结合结构域在全局运动模式中以其高迁移率为特征，这是识别位点的典型特征，在其他蛋白质中也有观察到。tRNA和GlnRS的大多数保守碱基和残基在分子的全局运动中受到严重限制，这表明它们在稳定和调节全局运动中发挥作用。
