蛋白质结构中的不允许的斑点
1Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar 824236, India.
Biochimica et biophysica acta. General subjects
|October 21, 2023
概括
用于蛋白质结构分析的Ramachandran地图,在高质量的蛋白质数据中没有显示任何不允许的 conformations. 蛋白质中不允许的斑点通常是由于相互作用或短环,而不是固有的残留物质.
科学领域:
- 结构生物学 结构生物学
- 生物物理学的生物物理.
- 计算生物学 计算生物学
背景情况:
- 1963年建立的Ramachandran (φ, ψ) 固态地图定义了蛋白质结构的可用构造空间.
- 在地图上禁止使用高能量的区域观察到蛋白质残留物促使进一步调查.
研究的目的:
- 为了明确地识别和描述蛋白质结构中不允许的残留形状的位置.
- 调查导致这些高能量状态中残留物发生的因素.
主要方法:
- 对36个高分辨率 (≤1 Å,R ≤0.10) 无噪声蛋白质结构进行分析,以确定不允许的 conformations.
- 对更大的数据集 (≤1.5 Å) 的检查,不包括模型错误和障碍.
- 符合性采样和残留物相互作用的分析.
主要成果:
- 在高质量,无噪声的蛋白质数据集中没有发现任何不允许的构造.
- 在短环 (3-5个残留物) 和相互作用点 (二硫化物键,内部/分子间相互作用) 确定了不允许的斑点.
- 相互作用中的残留物在相互作用被移除后减轻了应变;短循环显示出有限的应变减轻.
结论:
- 高能不允许的形状不是固有的特定残留物,而是来自特定的结构上下文,如短环或稳定相互作用.
- 像pre-Pro,Ser,Asp,trans-Pro,Val,Asn和Gly这样的残留物可能出现在不允许的区域中,这是由于结构限制和稳定相互作用.
- 这项研究完善了对蛋白质构造空间的理解,以及将残留物推向高能量状态的因素.
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