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Sequence analysis on the information of folding initiation segments in ferredoxin-like fold proteins.
BMC Structural Biology Pub Date : 2014-05-23 , DOI: 10.1186/1472-6807-14-15
Masanari Matsuoka , Takeshi Kikuchi 1
Affiliation  

BACKGROUND While some studies have shown that the 3D protein structures are more conservative than their amino acid sequences, other experimental studies have shown that even if two proteins share the same topology, they may have different folding pathways. There are many studies investigating this issue with molecular dynamics or Go-like model simulations, however, one should be able to obtain the same information by analyzing the proteins' amino acid sequences, if the sequences contain all the information about the 3D structures. In this study, we use information about protein sequences to predict the location of their folding segments. We focus on proteins with a ferredoxin-like fold, which has a characteristic topology. Some of these proteins have different folding segments. RESULTS Despite the simplicity of our methods, we are able to correctly determine the experimentally identified folding segments by predicting the location of the compact regions considered to play an important role in structural formation. We also apply our sequence analyses to some homologues of each protein and confirm that there are highly conserved folding segments despite the homologues' sequence diversity. These homologues have similar folding segments even though the homology of two proteins' sequences is not so high. CONCLUSION Our analyses have proven useful for investigating the common or different folding features of the proteins studied.

中文翻译:

铁氧还蛋白样折叠蛋白折叠起始片段信息的序列分析。

背景虽然一些研究表明,3D 蛋白质结构比它们的氨基酸序列更保守,但其他实验研究表明,即使两种蛋白质具有相同的拓扑结构,它们也可能具有不同的折叠途径。有许多研究使用分子动力学或类似 Go 的模型模拟来研究这个问题,但是,如果序列包含有关 3D 结构的所有信息,则应该能够通过分析蛋白质的氨基酸序列来获得相同的信息。在这项研究中,我们使用有关蛋白质序列的信息来预测其折叠片段的位置。我们专注于具有铁氧还蛋白样折叠的蛋白质,其具有特征拓扑结构。其中一些蛋白质具有不同的折叠片段。结果 尽管我们的方法很简单,通过预测被认为在结构形成中起重要作用的致密区域的位置,我们能够正确确定实验确定的折叠段。我们还将我们的序列分析应用于每种蛋白质的一些同源物,并确认尽管同源物具有序列多样性,但仍存在高度保守的折叠片段。即使两个蛋白质的序列的同源性不是那么高,这些同源物也具有相似的折叠片段。结论我们的分析已证明对研究所研究蛋白质的共同或不同折叠特征很有用。我们还将我们的序列分析应用于每种蛋白质的一些同源物,并确认尽管同源物具有序列多样性,但仍存在高度保守的折叠片段。即使两个蛋白质的序列的同源性不是那么高,这些同源物也具有相似的折叠片段。结论我们的分析已证明对研究所研究蛋白质的共同或不同折叠特征很有用。我们还将我们的序列分析应用于每种蛋白质的一些同源物,并确认尽管同源物具有序列多样性,但仍存在高度保守的折叠片段。即使两个蛋白质的序列的同源性不是那么高,这些同源物也具有相似的折叠片段。结论我们的分析已证明对研究所研究蛋白质的共同或不同折叠特征很有用。
更新日期:2019-11-01
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