Clarke N D
Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.
Protein Sci. 1995 Nov;4(11):2269-78. doi: 10.1002/pro.5560041104.
Homeodomains are 60 amino acid DNA binding domains found in numerous eukaryotic transcription factors. The homeodomain family is a useful system for studying sequence-structure relationships because several hundred sequences are known and the structures of several homeodomains have been determined. Covariation of amino acid residues in the homeodomain family has been investigated to see whether strongly covariant residue pairs can be understood in terms of the structure and function of these domains. Among 16 strongly covariant pairs examined, 2 are explained by the ability to form salt bridges, and 9 appear related to the DNA binding function of the proteins. For the remaining 5 pairs, the rationale for covariance remains unclear and the likelihood of artifactual correlations is discussed in the context of experimental and evolutionary biases in the selection of sequences. No significant correlation was found between covariance and structural proximity in the hydrophobic core.
同源结构域是在众多真核转录因子中发现的由60个氨基酸组成的DNA结合结构域。同源结构域家族是研究序列-结构关系的一个有用系统，因为已知数百个序列，并且已经确定了几个同源结构域的结构。人们研究了同源结构域家族中氨基酸残基的共变情况，以了解是否能根据这些结构域的结构和功能来理解强共变残基对。在研究的16对强共变对中，2对可通过形成盐桥的能力来解释，9对似乎与蛋白质的DNA结合功能有关。对于其余5对，共变的原理尚不清楚，并且在序列选择中的实验和进化偏差的背景下讨论了人为相关性的可能性。在疏水核心中，共变与结构接近度之间未发现显著相关性。
