蛋白演化只是在缓慢地发生，因为大部分氨基酸替换都可能是有害的，而且选择性将有利于功能的保持。Inna Povolotskaya 和 Fyodor Kondrashov试图搞清楚这个过程到底有多慢，他们的办法是，提出这样一个问题：古老的现存蛋白——即那些存在于“最后普遍共同祖先”(LUCA)身上的蛋白——是否在继续从先祖序列分化？
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他们所采用的方法是Edwin Hubble在其关于宇宙中星系退行的研究中所用的方法，其结论表明，现存蛋白序列仍然在从相互之间扩展，因此也在从共同祖先扩展。分化的速度是非常慢的：35亿年左右，因为LUCA的时间还没有长到达到序列分化极限的程度。这种缓慢性是序列空间中的功能性蛋白序列稀少以及蛋白适应性非常强所造成的：98%的点不能在一个给定的时刻接受一个氨基酸替换，而当其他互补性变化发生时，大多数点最终会被允许发生演化。(生物谷Bioon.net)
生物谷推荐原文出处：
Nature doi:10.1038/nature09105
Sequence space and the ongoing expansion of the protein universe
Inna S. Povolotskaya & Fyodor A. Kondrashov
The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions1, 2, 3, 4. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: ~98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, ~3.5?×?109?yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.
