Codon number shapes peptide redundancy in the universal proteome composition
Codon number shapes peptide redundancy in the universal proteome composition
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DOI：
10.1016/j.peptides.2009.06.035
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发表时间：
2009-10-01
期刊：
影响因子：
3
通讯作者：
Kanduc, Darja
中科院分区：
文献类型：
--
作者：
Kusalik, Anthony;Trost, Brett;Kanduc, Darja
将UniRef100数据库中编目的蛋白质组收集到单个蛋白质组集中，并检查实际与理论五肽的出现。我们发现了高度多样化的五肽冗余度。从数字上看，953个五聚体在蛋白质世界中只表达一次，而103个五聚体出现超过50，000次。此外，似乎有417种潜在的五肽不存在于蛋白质世界中。总的来说，跟踪的冗余配置文件的蛋白质世界的五肽出现的函数揭示了一个准高斯曲线，尾巴代表几乎没有和重复出现的5聚体。理化生物学参数分析表明，密码子数目是影响和支持通用蛋白质组组成中特定五肽频率的主要因素。也就是说，当与从未表达的5聚体的集合相比时，在通用蛋白质组中经常表示的五肽被赋予更多数量的多密码子氨基酸。相比之下，蓬松度和疏水性水平起的作用较小。出乎意料的是，五肽的形成热似乎影响最小。(C)2009 Elsevier Inc. All rights reserved.
The proteomes catalogued in the UniRef100 database were collected into a single proteome set and examined for actual versus theoretical pentapeptide occurrences. We found a highly diversified degree of pentapeptide redundancy. Numerically, 953 pentamers are expressed only once in the protein world, whereas 103 pentamers; occur more than 50,000 times. Moreover, it seems that 417 potentially possible pentapeptides are not present in the protein world. On the whole, tracing the redundancy profile of the protein world as a function of pentapeptide occurrences reveals a quasi-Gaussian curve, with tails representing scarcely and repeatedly occurring 5-mers. Analysis of physico-chemical-biological parameters shows that codon number is the main factor influencing and favoring specific pentapeptide frequencies in the universal proteome composition. That is, when compared to the set of never-expressed 5-mers, the pentapeptides frequently represented in the universal proteome are endowed with a higher number of multi-codonic amino acids. In contrast, the bulkiness degree and the hydrophobicity level play a smaller role. Unexpectedly, the heat of formation of pentapeptide appears to have the least influence. (C) 2009 Elsevier Inc. All rights reserved.