OCCURRENCE AND ROLE OF CIS PEPTIDE-BONDS IN PROTEIN STRUCTURES
OCCURRENCE AND ROLE OF CIS PEPTIDE-BONDS IN PROTEIN STRUCTURES
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DOI：
10.1016/0022-2836(90)90159-j
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发表时间：
1990-07-05
影响因子：
5.6
通讯作者：
WAMPLER, JE
中科院分区：
文献类型：
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作者：
STEWART, DE;SARKAR, A;WAMPLER, JE
人们普遍认为，由于这种同分异构体中相邻氨基酸残基之间的不利接触，顺式肽键在蛋白质中的出现是相当罕见的。为了研究这一假设，布鲁克海文蛋白质数据库检查了顺式肽键的出现。在31,005个酰胺键中，只有17个（0.05%）是顺式的，而1534个亚胺键（X-Pro）中有99个（6.5%）是顺式的。这些数字远远小于根据顺式和反式异构体形式之间的势能差和小肽的实验数据预测的分布。目前尚不清楚顺肽键低于预期的出现是由于蛋白质环境施加的限制，还是由于在x射线晶体结构溶液中做出的假设。然而，当相对于结构的分辨率检查数据库中顺式键的出现时，顺式键的数量随着分辨率的增加而增加。这些肽的分布。数据库中的化学键与简单势能势垒预测的分布形状不同。它们在主体上更锋利，但在基部也更宽，具有大量的非平面肽键。顺式肽键主要在弯曲和旋转中发现，在顺式亚胺键（X-PRO）的情况下，这种相关性如此之高，以至于它表明顺式亚胺基团在这种结构中起着特定的作用。
It has been widely assumed that the occurrence of cis peptide bonds in proteins is quite rare due to unfavorable contacts between adjacent amino acid residues in this isomeric form. To investigate this assumption, the Brookhaven Protein Data Bank was examined for the occurrences of cis peptide bonds. Out of 31,005 amide bonds, only 17, or 0.05%, are cis, while 99 of the 1534 imide bonds (X-Pro), or 6.5%, are cis. These figures are considerably less than the distribution predicted on the basis of the potential energy difference between the cis and trans isomeric forms and experimental data on small peptides. It is not know whether the lower than expected occurrence of cis peptide bonds arises from constraints imposed by the protein environment, or from assumptions made in the solution of X-ray crystal structures. However, when the occurrence of cis bonds in the data base is examined relative to the resolution of the structure, the number of cis bonds increases with increasing resolution. The distributions seen for these peptide .omega. bonds in the data base are not the same shape as the distributions predicted from simple potential energy barriers. They are sharper in the main, but they are also broader at the base with significant numbers of non-planar peptide bonds. Cis peptide bonds are found primarily in bends and turns and, in the case of cis imide bonds (X-PRO), this correlation is so high that it suggests a specific role for cis imide groups in such structures.