Anderson Robert J, Weng Zhiping, Campbell Robert K, Jiang Xuliang
Serono Reproductive Biology Institute, One Technology Place, Rockland, Massachusetts, USA.
Proteins. 2005 Sep 1;60(4):679-89. doi: 10.1002/prot.20530.
A Ramachandran plot is a visual representation of the main-chain conformational tendencies of an amino acid. Despite forty years of research, the shape of Ramachandran plots is still a matter of debate. The issue in making a Ramachandran plot based on experimental data is deciding whether sparse data represent genuine conformations. We present here a simple solution to settle the ambiguities of the sparse data, and explain how we verified the accuracies of our plots using an independent dataset. To obtain our results, we then measured the pair-wise distances of main-chain conformational tendencies among amino acids, and showed that the conformational relationships of amino acids are well preserved in a two-dimensional map, leading to the conclusion that the conformational diversity space of amino acids is largely two dimensional. We further noticed that amino acids in early and late evolutionary stages are located in different zones in the two-dimensional map. In addition to these conclusions, we here present an amino acid substitution table derived from experimental data.
拉马钱德兰图是氨基酸主链构象倾向的直观表示。尽管经过了四十年的研究，但拉马钱德兰图的形状仍然存在争议。基于实验数据制作拉马钱德兰图的问题在于确定稀疏数据是否代表真实构象。我们在此提出一个简单的解决方案来解决稀疏数据的模糊性，并解释我们如何使用独立数据集验证我们的图的准确性。为了获得我们的结果，我们随后测量了氨基酸之间主链构象倾向的成对距离，并表明氨基酸的构象关系在二维图中得到了很好的保留，从而得出氨基酸的构象多样性空间在很大程度上是二维的结论。我们还进一步注意到，处于进化早期和晚期的氨基酸位于二维图中的不同区域。除了这些结论，我们在此展示了一个从实验数据得出的氨基酸替换表。
