ALIGNMENT OF 700 GLOBIN SEQUENCES - EXTENT OF AMINO-ACID SUBSTITUTION AND ITS CORRELATION WITH VARIATION IN VOLUME

被引:83
作者
KAPP, OH
MOENS, L
VANFLETEREN, J
TROTMAN, CNA
SUZUKI, T
VINOGRADOV, SN
机构
[1] UNIV CHICAGO, DEPT RADIOL, CHICAGO, IL 60637 USA
[2] UNIV INSTELLING ANTWERP, DEPT BIOCHEM, B-2610 WILRIJK, BELGIUM
[3] STATE UNIV GHENT, MORPHOL & SYSTEMAT LAB, B-9000 GHENT, BELGIUM
[4] UNIV OTAGO, DEPT BIOCHEM, DUNEDIN, NEW ZEALAND
[5] KOCHI UNIV, DEPT BIOL, KOCHI 780, JAPAN
[6] WAYNE STATE UNIV, SCH MED, DEPT BIOCHEM, DETROIT, MI 48201 USA
关键词
AMINO ACID SUBSTITUTION; GLOBIN; NONVERTEBRATE; SEQUENCES; VERTEBRATE;
D O I
10.1002/pro.5560041024
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:2179 / 2190
页数:12
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