ALIGNMENT OF 700 GLOBIN SEQUENCES - EXTENT OF AMINO-ACID SUBSTITUTION AND ITS CORRELATION WITH VARIATION IN VOLUME
ALIGNMENT OF 700 GLOBIN SEQUENCES - EXTENT OF AMINO-ACID SUBSTITUTION AND ITS CORRELATION WITH VARIATION IN VOLUME
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DOI：
10.1002/pro.5560041024
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发表时间：
1995-10-01
期刊：
影响因子：
8
通讯作者：
VINOGRADOV, SN
中科院分区：
文献类型：
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作者：
KAPP, OH;MOENS, L;VINOGRADOV, SN
700 个珠蛋白序列，包括 146 个非脊椎动物序列，在二级结构保守和避免缺口罚分的基础上进行了比对。在容纳所有珠蛋白序列所需的 182 个位置中，只有 84 个是共有的，包括绝对保守的 PheCD1 和 HisF8。所有珠蛋白每个位置的平均氨基酸取代数范围为 8 至 13 个，内部位置的平均氨基酸取代数为 5 至 9 个。尽管总序列体积的变化类似于 2-3%，但每个位置的体积变化范围从内部位置的大约 13% 到表面位置的大约 21%。对于 84 个常见位置和内部位置（而非表面位置），氨基酸取代与每个位置的体积变化之间存在合理的相关性。衍生自 84 个共同位置的氨基酸取代矩阵用于通过计算成对相似性得分来评估球蛋白内以及球蛋白与藻蓝蛋白 C 和大肠杆菌素 A 之间的序列相似性。 84 个常见位置的球蛋白-球蛋白比较得分与球蛋白-藻蓝蛋白和球蛋白-大肠菌素得分重叠，前者处于中间位置。对于内部位置的子集，三组分数之间的重叠最小。这些结果意味着氨基酸序列的连续体能够呈现常见的三对三α螺旋结构，并表明后者的决定因素包括除溶剂不可及的位点之外的位点。
Seven-hundred globin sequences, including 146 nonvertebrate sequences, were aligned on the basis of conservation of secondary structure and the avoidance of gap penalties. Of the 182 positions needed to accommodate all the globin sequences, only 84 are common to all, including the absolutely conserved PheCD1 and HisF8. The mean number of amino acid substitutions per position ranges from 8 to 13 for all globins and 5 to 9 for internal positions. Although the total sequence volumes have a variation similar to 2-3%, the variation in volume per position ranges from similar to 13% for the internal to similar to 21% for the surface positions. Plausible correlations exist between amino acid substitution and the variation in volume per position for the 84 common and the internal but not the surface positions. The amino acid substitution matrix derived from the 84 common positions was used to evaluate sequence similarity within the globins and between the globins and phycocyanins C and colicins A, via calculation of pairwise similarity scores. The scores for globin-globin comparisons over the 84 common positions overlap the globin-phycocyanin and globin-colicin scores, with the former being intermediate. For the subset of internal positions, overlap is minimal between the three groups of scores. These results imply a continuum of amino acid sequences able to assume the common three-on-three alpha-helical structure and suggest that the determinants of the latter include sites other than those inaccessible to solvent.