Protein packing: Dependence on protein size, secondary structure and amino acid composition
Protein packing: Dependence on protein size, secondary structure and amino acid composition
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DOI：
10.1006/jmbi.2000.3750
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发表时间：
2000-06-02
影响因子：
5.6
通讯作者：
Richards, FM
中科院分区：
文献类型：
--
作者：
Fleming, PJ;Richards, FM
我们已经使用遮挡面算法来估计蛋白质结构中埋藏和暴露的氨基酸残基的包装。这种方法对埋藏残留物和溶剂暴露残留物同样有效，而常用的Voronoi方法只对埋藏残留物直接有效。单个球状蛋白的原子排列可能与大量球状蛋白数据集的平均排列有很大不同。在这里，我们证明了蛋白质包装的这些变化是由于蛋白质大小、二级结构组成和氨基酸组成的复杂组合。在结构相似的蛋白家族中，尽管有显著的序列差异，但蛋白质包装的差异是保守的。这一结论表明，蛋白质结构包装的质量评估应包括考虑各种参数，包括已知同源蛋白的包装。此外，基于同源模板的蛋白质结构建模应考虑模板蛋白质结构的包装。(C) 2000年学术出版社。
We have used the occluded surface algorithm to estimate the packing of both buried and exposed amino acid residues in protein structures. This method works equally well for buried residues and solvent-exposed residues in contrast to the commonly used Voronoi method that works directly only on buried residues. The atomic packing of individual globular proteins may vary significantly from the average packing of a large data set of globular proteins. Here, we demonstrate that these variations in protein packing are due to a complex combination of protein size, secondary structure composition and amino acid composition. Differences in protein packing are conserved in protein families of similar structure despite significant sequence differences. This conclusion indicates that quality assessments of packing in protein structures should include a consideration of various parameters including the packing of known homologous proteins. Also, modeling of protein structures based on homologous templates should take into account the packing of the template protein structure. (C) 2000 Academic Press.