难以调整内在无序的蛋白质序列的困难,根据保护和分化学来评估
Andrew C Riley1,2, Daniel A Ashlock1,3, Steffen P Graether1,2
1Graduate Program in Bioinformatics, University of Guelph, Guelph, Ontario, Canada.
PloS one
|July 13, 2023
概括
内在无序的蛋白质 (IDP) 显示出较少的对齐一致性比有序的蛋白质由于较低的序列保存. 然而,它们的排列仍然准确地重建了物种树,表明质量很好.
科学领域:
- 蛋白质组学是指蛋白质组学.
- 生物信息学是一种生物信息学.
- 进化生物学 进化生物学
背景情况:
- 内在无序的蛋白质 (IDP) 缺乏稳定的3D结构,但在功能上很重要.
- 假设IDP由于减少了序列保存,因此很难对齐.
- 这种难以调整内部发展计划的困难还没有经验验证.
研究的目的:
- 直接比较内在无序蛋白质 (IDP) 与有序蛋白质的多重序列对齐 (MSA) 质量.
- 用MSA一致性和族系信号重建来评估对齐的正确性.
- 调查IDP中较低序列保存是否影响对齐质量.
主要方法:
- 使用Clustal Omega,MAFFT和MUSCLE.生成了有序,无序和混合蛋白质的多重序列对齐 (MSA).
- 通过比较不同对齐方法之间的相似性 (一致性) 来评估MSA正确性.
- 通过评估它们对已知物种树的总结程度 (系遗传信号) 来评估MSA的正确性.
- 分析了核酸,密码子和序列对齐.
主要成果:
- 固有无序蛋白质 (IDP) 的多重序列对齐 (MSA) 比有序蛋白质的多重序列对齐 (MSA) 不那么一致.
- 在IDP对齐中这种减少的一致性与较低的序列保存相关.
- 从IDP对齐推断的家族遗传树在重建物种树方面并不明显差,而不是从有序蛋白质中推断的.
结论:
- 固有无序蛋白质 (IDP) 的确更难以根据对齐一致性指标进行对齐.
- 这种困难并不一定意味着对齐质量差,因为IDP对齐仍然可以准确地反映家族遗传关系.
- 调整策略应考虑IDP的独特属性,以便可靠地推断遗传学推理.
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