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直接从自旋弛豫数据快速推断蛋白质骨架旋转动力学。

Rapid Interpretation of Protein Backbone Rotation Dynamics Directly from Spin Relaxation Data.

机构信息

Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland.

Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland.

出版信息

J Phys Chem Lett. 2024 Oct 10;15(40):10204-10209. doi: 10.1021/acs.jpclett.4c01800. Epub 2024 Oct 1.

Abstract

Besides their structure, dynamics is pivotal for protein functions, particularly for intrinsically disordered proteins (IDPs) that do not fold into a fixed 3D structure. However, the detection of protein dynamics is difficult for IDPs and other disordered biomolecules. NMR spin relaxation rates are sensitive to the rapid rotations of chemical bonds, but their interpretation is arduous for IDPs or molecular assemblies with a complex dynamic landscape. Here we demonstrate numerically that the dynamics of a wide range of proteins, from short peptides to partially disordered proteins and peptides in micelles, can be characterized by calculating the total effective correlation times of protein backbone N-H bond rotations, τ, from experimentally measured transverse N spin relaxation rates, , using a linear relation. Our results enable the determination of magnetic-field-independent and intuitively understandable parameters describing protein dynamics at different regions of the sequence directly from experiments. A practical advance of the approach is demonstrated by analyzing partially disordered proteins in which rotations of disordered regions occur with timescales of 1-2 ns, independent of their size, suggesting that rotations of disordered and folded regions are uncoupled in these proteins.

摘要

除了结构,动力学对于蛋白质功能至关重要,特别是对于没有折叠成固定 3D 结构的无规卷曲蛋白质(IDP)。然而,IDP 和其他无规生物分子的蛋白质动力学检测非常困难。NMR 自旋弛豫率对化学键的快速旋转很敏感,但对于 IDP 或具有复杂动态景观的分子组装体,其解释非常困难。在这里,我们通过数值证明,从短肽到胶束中部分无序的蛋白质和肽等广泛的蛋白质的动力学可以通过计算从实验测量的横向 N 自旋弛豫率 ,使用线性关系来表征蛋白质骨架 N-H 键旋转的总有效相关时间 τ。我们的结果使人们能够从实验中直接确定描述序列不同区域的磁场独立且直观的蛋白质动力学参数。通过分析其中无序区域的旋转在 1-2ns 的时间范围内发生的部分无序蛋白质,该方法的实际进展得到了证明,这与它们的大小无关,这表明这些蛋白质中无序区和折叠区的旋转是解耦的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/daff/11480883/3a31cbbc13e5/jz4c01800_0001.jpg

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