The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand.
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand.
复制标题
DOI：
10.1186/1471-2105-11-383
复制
发表时间：
2010-07-20
影响因子：
3
通讯作者：
Kanduc D
中科院分区：
文献类型：
--
作者：
Capone G;Novello G;Fasano C;Trost B;Bickis M;Kusalik A;Kanduc D
我们研究了特定肽平台在蛋白质组成中的使用。使用五肽作为长度单位，我们发现在通用蛋白质组中，许多五肽被大量重复（甚至数千次），而有些则非常罕见，少数根本不出现。为了了解蛋白质组水平上肽使用的物理-化学-生物学基础，在这项研究中，我们分析了罕见的和从未表达的与常见的五肽合成的能量成本。此外，我们探讨残基体积，疏水性，和密码子数量的因素能够调节特定的肽频率。然后，氨基酸组成的可能影响进行了研究，在零和高频率的五肽组通过分析相应的反向序列五肽的频率。作为最后一步，我们分析了十五聚体寡脱氧核苷酸序列对应的从未表达的五肽。我们发现，只有DNA上下文相关的约束（如寡脱氧核苷酸序列在负链，内含子，假基因，移码等位置），提供了一个连贯的机制平台来解释在蛋白质世界中从未表达的五肽与频繁表达的五肽的发生。这项研究在细胞生物学中具有重要意义。实际上，特定5-mer肽模块的稀有性（或缺乏表达）暗示相应的n-mer肽序列（其中n < 5）的稀有性（或缺乏表达），因此可能调节蛋白质组成趋势。此外，这些数据可能进一步加深我们对稀有五肽模块在蛋白质-蛋白质相互作用中作为关键生物效应器所发挥的作用的理解。
We study the usage of specific peptide platforms in protein composition. Using the pentapeptide as a unit of length, we find that in the universal proteome many pentapeptides are heavily repeated (even thousands of times), whereas some are quite rare, and a small number do not appear at all. To understand the physico-chemical-biological basis underlying peptide usage at the proteomic level, in this study we analyse the energetic costs for the synthesis of rare and never-expressed versus frequent pentapeptides. In addition, we explore residue bulkiness, hydrophobicity, and codon number as factors able to modulate specific peptide frequencies. Then, the possible influence of amino acid composition is investigated in zero- and high-frequency pentapeptide sets by analysing the frequencies of the corresponding inverse-sequence pentapeptides. As a final step, we analyse the pentadecamer oligodeoxynucleotide sequences corresponding to the never-expressed pentapeptides. We find that only DNA context-dependent constraints (such as oligodeoxynucleotide sequence location in the minus strand, introns, pseudogenes, frameshifts, etc.) provide a coherent mechanistic platform to explain the occurrence of never-expressed versus frequent pentapeptides in the protein world. This study is of importance in cell biology. Indeed, the rarity (or lack of expression) of specific 5-mer peptide modules implies the rarity (or lack of expression) of the corresponding n-mer peptide sequences (with n < 5), so possibly modulating protein compositional trends. Moreover the data might further our understanding of the role exerted by rare pentapeptide modules as critical biological effectors in protein-protein interactions.
登录
查看更多内容
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
6.4
作者：
Mittelman, A;Lucchese, A;Kanduc, D
通讯作者：
Kanduc, D
影响因子：
3
作者：
Kusalik, Anthony;Trost, Brett;Kanduc, Darja
通讯作者：
Kanduc, Darja
影响因子：
10.7
作者：
Brooks, DJ;Fresco, JR;Singh, M
通讯作者：
Singh, M
影响因子：
3
作者：
Kanduc, D;Lucchese, A;Mittelman, A
通讯作者：
Mittelman, A