Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context.
Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context.
复制标题
细胞色素 c 氧化酶亚基 I 的共同进化模式取决于结构和功能背景。
DOI：
10.1007/s00239-007-9018-8
复制
发表时间：
2007
影响因子：
3.9
通讯作者：
Pollock,DavidD
中科院分区：
文献类型：
--
作者：
Wang,ZhengyuanO;Pollock,DavidD
氨基酸残基之间的协同进化强度和模式因其结构和功能环境而异。这种上下文依赖性，以及分析技术的差异，是不同蛋白质共同进化分析结果不同的原因。因此，重要的是对单个蛋白质进行详细的研究，以更好地了解上下文依赖如何影响共同进化模式，甚至在单个蛋白质中也是如此，并从结构和功能方面揭示上下文依赖的细节。在这里，我们进一步分析了231种脊椎动物细胞色素氧化酶亚基I序列中的残基协同进化，并使用了一种基于系统发育的统计稳健的最大似然比方法来扩展我们之前的研究。与以往的研究一样，检测到了一个强烈的整体协同进化信号，结构区域内的协同进化与残基之间的Cα距离显著相关。虽然在表面区预测的协同进化对中对相邻残基的强烈选择表明该统计方法对生物相关的相互作用具有高度的选择性，但在跨膜区的协同进化信号最强，尽管协同进化残基之间的距离较大。这表明共同进化可能在跨膜区维持更多的全局结构和功能限制。在跨膜区，根据极性和疏水性而不是体积共同进化的位点更有可能只与一个预测的质子通道(H通道)共存。因此，细胞色素氧化酶亚基I的协同进化的细节在很大程度上取决于结构域结构和残基的理化特性，但与功能的接近似乎起着关键作用。我们假设，共同进化表明这一通道具有更重要的功能作用。
The strength and pattern of coevolution between amino acid residues vary depending on their structural and functional environment. This context dependence, along with differences in analytical technique, is responsible for the different results among coevolutionary analyses of different proteins. It is thus important to perform detailed study of individual proteins to gain better insight into how context dependence can affect coevolutionary patterns even within individual proteins, and to unravel the details of context dependence with respect to structure and function. Here we extend our previous study by presenting further analysis of residue coevolution in cytochromecoxidase subunit I sequences from 231 vertebrates using a statistically robust phylogeny-based maximum likelihood ratio method. As in previous studies, a strong overall coevolutionary signal was detected, and coevolution within structural regions was significantly related to the Cαdistances between residues. While the strong selection for adjacent residues among predicted coevolving pairs in the surface region indicates that the statistical method is highly selective for biologically relevant interactions, the coevolutionary signal was strongest in the transmembrane region, although the distances between coevolving residues were greater. This indicates that coevolution may act to maintain more global structural and functional constraints in the transmembrane region. In the transmembrane region, sites that coevolved according to polarity and hydrophobicity rather than volume had a greater tendency to colocalize with just one of the predicted proton channels (channel H). Thus, the details of coevolution in cytochromecoxidase subunit I depend greatly on domain structure and residue physicochemical characteristics, but proximity to function appears to play a critical role. We hypothesize that coevolution is indicative of a more important functional role for this channel.