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基于集合的结构计算,利用精确 NOE 对蛋白质中的运动进行空间解析。

Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs.

机构信息

Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich, Switzerland.

出版信息

Nat Struct Mol Biol. 2012 Oct;19(10):1053-7. doi: 10.1038/nsmb.2355. Epub 2012 Sep 2.

Abstract

Proteins are inherently dynamic systems whose motions cover large ranges in both magnitude and timescale. Because of the omnipresence of motion, it is likely that dynamics have important roles in the function of biomolecules. For detailed understanding of a protein's function, the three-dimensional structure and description of its dynamics are therefore required. Structure determination methods are well established, and NMR-relaxation phenomena provide insights into local molecular dynamics; moreover, recently several attempts have been made to detect concerted motion. Here, we present an ensemble-based structure-determination protocol using ensemble-averaged distance restraints obtained from exact NOE rates. Application to the model protein GB3 establishes an ensemble of structures that reveals correlated motion across the β-sheet, concerted motion between the backbone and side chains localized in the structure core, and a lack of concerted conformational exchange between the β-sheet and the α-helix.

摘要

蛋白质是固有动态系统,其运动在幅度和时间尺度上都有很大的范围。由于运动无处不在,因此动力学很可能在生物分子的功能中发挥重要作用。为了详细了解蛋白质的功能,因此需要对其三维结构和动力学描述。结构确定方法已经成熟,NMR 弛豫现象提供了对局部分子动力学的深入了解;此外,最近已经有一些尝试来检测协同运动。在这里,我们提出了一种基于集合的结构确定方案,该方案使用从精确 NOE 速率获得的集合平均距离约束。将其应用于模型蛋白 GB3,确定了一组结构,这些结构揭示了β-折叠之间的相关运动,结构核心中骨架和侧链之间的协同运动,以及β-折叠和α-螺旋之间缺乏协同构象交换。

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