Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
J Phys Chem B. 2021 Mar 11;125(9):2212-2221. doi: 10.1021/acs.jpcb.0c10188. Epub 2021 Feb 26.
Understanding and describing the dynamics of proteins is one of the major challenges in biology. Here, we use multifield variable-temperature NMR longitudinal relaxation (R) measurements to determine the hierarchical activation energies of motions of four different proteins: two small globular proteins (GB1 and the SH3 domain of α-spectrin), an intrinsically disordered protein (the C-terminus of the nucleoprotein of the Sendai virus, Sendai Ntail), and an outer membrane protein (OmpG). The activation energies map the motions occurring in the side chains, in the backbone, and in the hydration shells of the proteins. We were able to identify similarities and differences in the average motions of the proteins. We find that the NMR relaxation properties of the four proteins do share similar features. The data characterizing average backbone motions are found to be very similar, the same for methyl group rotations, and similar activation energies are measured. The main observed difference occurs for the intrinsically disordered Sendai Ntail, where we observe much lower energy of activation for motions of protons associated with the protein-solvent interface as compared to the others. We also observe variability between the proteins regarding side chain N relaxation of lysine residues, with a higher activation energy observed in OmpG. This hints at strong interactions with negatively charged lipids in the bilayer and provides a possible mechanistic clue for the "positive-inside" rule for helical membrane proteins. Overall, these observations refine the understanding of the similarities and differences between hierarchical dynamics in proteins.
理解和描述蛋白质的动力学是生物学中的主要挑战之一。在这里，我们使用多场变温 NMR 纵向弛豫（R）测量来确定四种不同蛋白质的运动的层次激活能：两个小的球形蛋白质（GB1 和 α- spectrin 的 SH3 结构域）、一个固有无序的蛋白质（仙台病毒核蛋白的 C 末端，Sendai Ntail）和一个外膜蛋白（OmpG）。这些激活能描绘了蛋白质侧链、骨架和水合壳中的运动。我们能够识别出蛋白质平均运动之间的相似性和差异性。我们发现，四种蛋白质的 NMR 弛豫性质确实具有相似的特征。表征平均骨架运动的数据非常相似，甲基旋转也是如此，并且测量到相似的激活能。主要的观察到的差异发生在固有无序的 Sendai Ntail 中，我们观察到与蛋白质-溶剂界面相关的质子运动的激活能要低得多，与其他蛋白质相比。我们还观察到不同蛋白质的赖氨酸残基侧链 N 弛豫之间存在可变性，OmpG 中观察到更高的激活能。这暗示了与双层中带负电荷的脂质之间存在强烈相互作用，并为螺旋膜蛋白的“正内”规则提供了可能的机制线索。总体而言，这些观察结果细化了对蛋白质层次动力学之间相似性和差异性的理解。
