Merlino Antonello, Sica Filomena, Mazzarella Lelio
Dipartimento di Chimica, Università degli Studi di Napoli Federico I", Via Cynthia, 80126 Napoli, Italy.
J Phys Chem B. 2007 May 17;111(19):5483-6. doi: 10.1021/jp071399h. Epub 2007 Apr 13.
Low-frequency internal motions in protein molecules play a key role in biological functions. A direct relationship between low-frequency motions and enzymatic activity has been suggested for bovine pancreatic ribonuclease (RNase A). The flexibility-function relationship in this enzyme has been attributed to a subtle and concerted breathing motion of the beta-sheet regions occurring upon substrate binding and release. Here, we calculate an approximate value for the force constant and the wave number of the low-frequency beta-sheet breathing motion of RNase A, by using the Boltzmann hypothesis on a set of data derived from a simple conventional structural superimposition of an unusual large number of X-ray structures available for the protein. The results agree with previous observations and with theoretical predictions on the basis of normal-mode analysis. To the best of our knowledge, this is the first example in which the wave number and the force constant of a low-frequency concerted motion in a protein are directly derived from X-ray structures.
蛋白质分子中的低频内部运动在生物学功能中起着关键作用。对于牛胰核糖核酸酶（RNase A），已有人提出低频运动与酶活性之间存在直接关系。该酶的柔韧性-功能关系归因于底物结合和释放时β-折叠区域发生的微妙且协同的呼吸运动。在此，我们利用玻尔兹曼假设，基于从该蛋白质大量可用的异常X射线结构的简单常规结构叠加中获得的一组数据，计算出RNase A低频β-折叠呼吸运动的力常数和波数的近似值。结果与先前的观察结果以及基于简正模式分析的理论预测相符。据我们所知，这是首个直接从X射线结构得出蛋白质中低频协同运动的波数和力常数的例子。
