Are residues in a protein folding nucleus evolutionarily conserved?
Are residues in a protein folding nucleus evolutionarily conserved?
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DOI：
10.1016/j.jmb.2003.11.007
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发表时间：
2003-11
影响因子：
5.6
通讯作者：
Y. Tseng;Jie Liang
中科院分区：
文献类型：
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作者：
Y. Tseng;Jie Liang
蛋白质是细胞的工作分子，进化是生命的标志。重要的是要了解蛋白质折叠和进化是如何相互影响的。几项将残基参与折叠核的实验测量与序列保守性相关的研究得出了不同的结论。这些研究是基于使用来自多序列比对的熵或相对熵测量来评估折叠核位置的序列保守性。在这里，我们报告了使用进化模型替代基于熵的方法来分析折叠核的守恒。我们使用密码子替换的连续时间马尔可夫模型来区分进化固定的突变和随机固定的突变。该模型考虑了密码子频率的偏差、偏向转换而不是颠换，以及明确的系统发育信息。我们使用单个残基上同义替换与非同义替换的比率ω来衡量选择压力。ω值是使用最大似然估计器PAML法估计的。我们的结果表明，由实验φ值衡量的蛋白质折叠核的动力学参与程度与由ω值衡量的选择压力之间几乎没有相关性。此外，两个随机试验均未显示折叠核残基明显比整个蛋白质更保守，或蛋白质中所有残基的中位数ω值。这些结果表明，在密码子替换水平上，没有迹象表明折叠核残基比其他残基更保守。我们进一步重建了折叠核的候选祖先残基，并建议进行可能的试管突变研究，以测试古代折叠核的折叠行为。
Protein is the working molecule of the cell, and evolution is the hallmark of life. It is important to understand how protein folding and evolution influence each other. Several studies correlating experimental measurement of residue participation in folding nucleus and sequence conservation have reached different conclusions. These studies are based on assessment of sequence conservation at folding nucleus sites using entropy or relative entropy measurement derived from multiple sequence alignment. Here we report analysis of conservation of folding nucleus using an evolutionary model alternative to entropy-based approaches. We employ a continuous time Markov model of codon substitution to distinguish mutation fixed by evolution and mutation fixed by chance. This model takes into account bias in codon frequency, bias-favoring transition over transversion, as well as explicit phylogenetic information. We measure selection pressure using the ratio ω of synonymous versus non-synonymous substitution at individual residue site. The ω-values are estimated using the PAML method, a maximum-likelihood estimator. Our results show that there is little correlation between the extent of kinetic participation in protein folding nucleus as measured by experimental φ-value and selection pressure as measured by ω-value. In addition, two randomization tests failed to show that folding nucleus residues are significantly more conserved than the whole protein, or the median ω value of all residues in the protein. These results suggest that at the level of codon substitution, there is no indication that folding nucleus residues are significantly more conserved than other residues. We further reconstruct candidate ancestral residues of the folding nucleus and suggest possible test tube mutation studies for testing folding behavior of ancient folding nucleus.