Wilbur W J
National Institute of Arthritis, Diabetes, Digestive, and Kidney Diseases, Bethesda, Maryland 20205.
Mol Biol Evol. 1985 Sep;2(5):434-47. doi: 10.1093/oxfordjournals.molbev.a040360.
The internal consistency of the PAM matrix model of protein evolution is here investigated. The 1 PAM matrix has been constructed from amino acid replacements observed in closely related sequences. Such replacements are of two types, those that do not require an intermediate amino acid replacement and those that do. The second type of replacement must generally be produced by a repetition of the first. This allows data on the first type to be used in predicting data on the second type so that some elements of the 1 PAM matrix may be used to predict others. A discrepancy of more than two orders of magnitude is found between the predictions and the data when this is carried out. This is partly accounted for by an error in constructing the matrix. However, it also seems necessary that the basic model be modified. Several possibilities are considered. One of these is to incorporate a site-dependent spectrum of mutabilities associated with each amino acid.
本文研究了蛋白质进化的PAM矩阵模型的内部一致性。1PAM矩阵是根据在密切相关序列中观察到的氨基酸替换构建的。这种替换有两种类型，一种是不需要中间氨基酸替换的，另一种是需要中间氨基酸替换的。第二种类型的替换通常必须通过第一种类型的重复产生。这使得第一种类型的数据可用于预测第二种类型的数据，从而1PAM矩阵的一些元素可用于预测其他元素。当进行此操作时，预测结果与数据之间发现了超过两个数量级的差异。这部分是由于构建矩阵时的误差造成的。然而，似乎也有必要修改基本模型。考虑了几种可能性。其中之一是纳入与每个氨基酸相关的位点依赖性突变谱。
