Westhof E, Dumas P, Moras D
Institut de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Strasbourg, France.
Acta Crystallogr A. 1988 Mar 1;44 ( Pt 2):112-23.
Four transfer RNA crystals, the monoclinic and orthorhombic forms of yeast tRNA(Phe) as well as forms A and B of yeast tRNA(Asp), have been submitted to the same restrained least-squares refinement program and refined to an R factor well below 20% for about 4500 reflections between 10 and 3 A. In yeast tRNA(Asp) crystals the molecules exist as dimers with base pairings of the anticodon (AC) triplets and labilization of the tertiary interaction between one invariant guanine of the dihydrouridine (D) loop and the invariant cytosine of the thymine (T) loop (G19-C56). In yeast tRNA(Phe) crystals, the molecules exist as monomers with only weak intermolecular packing contacts between symmetry-related molecules. Despite this, the tertiary folds of the L-shaped tRNA structures are identical when allowance is made for base sequence changes between tRNA(Phe) and tRNA(Asp). However, the relative mobilities of two regions are inverse in the two structures with the AC loop more mobile than the D loop in tRNA(Phe) and the D loop more mobile than the AC loop in tRNA(Asp). In addition, the T loop becomes mobile in tRNA(Asp). The present refinements were performed to exclude packing effects or refinement bias as possible sources of such differential dynamic behavior. It is concluded that the transfer of flexibility from the anticodon to the D- and T-loop region in tRNA(Asp) is not a crystal-line artefact. Further, analysis of the four structures supports a mechanism for the flexibility transfer through base stacking in the AC loop and concomitant variations in twist angles between base pairs of the anticodon helix which propagate up to the D- and T-loop region.
四种转运RNA晶体，即酵母苯丙氨酸转运RNA（tRNA(Phe)）的单斜晶系和正交晶系形式以及酵母天冬氨酸转运RNA（tRNA(Asp)）的A和B形式，已被提交至同一个约束最小二乘法精修程序，并针对10至3埃之间的约4500个反射，精修至R因子远低于20%。在酵母天冬氨酸转运RNA（tRNA(Asp)）晶体中，分子以二聚体形式存在，反密码子（AC）三联体之间形成碱基配对，二氢尿嘧啶（D）环的一个不变鸟嘌呤与胸腺嘧啶（T）环的不变胞嘧啶之间的三级相互作用（G19-C56）不稳定。在酵母苯丙氨酸转运RNA（tRNA(Phe)）晶体中，分子以单体形式存在，对称相关分子之间只有微弱的分子间堆积接触。尽管如此，当考虑到tRNA(Phe)和tRNA(Asp)之间的碱基序列变化时，L形tRNA结构的三级折叠是相同的。然而，在这两种结构中，两个区域的相对流动性是相反的，在tRNA(Phe)中AC环比D环更具流动性，而在tRNA(Asp)中D环比AC环更具流动性。此外，在tRNA(Asp)中T环变得具有流动性。进行目前的精修是为了排除堆积效应或精修偏差作为这种差异动态行为的可能来源。得出的结论是，tRNA(Asp)中灵活性从反密码子向D环和T环区域的转移不是晶体假象。此外，对这四种结构的分析支持了一种通过AC环中的碱基堆积以及反密码子螺旋碱基对之间扭转角的伴随变化来实现灵活性转移的机制，这种变化一直传播到D环和T环区域。
