Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.
University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France.
J Am Chem Soc. 2024 Mar 27;146(12):8164-8178. doi: 10.1021/jacs.3c12620. Epub 2024 Mar 13.
Side-chain motions play an important role in understanding protein structure, dynamics, protein-protein, and protein-ligand interactions. However, our understanding of protein side-chain dynamics is currently limited by the lack of analytical tools. Here, we present a novel analytical framework employing experimental nuclear magnetic resonance (NMR) relaxation measurements at atomic resolution combined with molecular dynamics (MD) simulation to characterize with a high level of detail the methyl side-chain dynamics in insoluble protein assemblies, using amyloid fibrils formed by the prion HET-s. We use MD simulation to interpret experimental results, where rotameric hops, including methyl group rotation and χ/χ rotations, cannot be completely described with a single correlation time but rather sample a broad distribution of correlation times, resulting from continuously changing local structure in the fibril. Backbone motion similarly samples a broad range of correlation times, from ∼100 ps to μs, although resulting from mostly different dynamic processes; nonetheless, we find that the backbone is not fully decoupled from the side-chain motion, where changes in side-chain dynamics influence backbone motion and vice versa. While the complexity of side-chain motion in protein assemblies makes it very challenging to obtain perfect agreement between experiment and simulation, our analytical framework improves the interpretation of experimental dynamics measurements for complex protein assemblies.
侧链运动在理解蛋白质结构、动力学、蛋白质-蛋白质和蛋白质-配体相互作用方面起着重要作用。然而，我们对蛋白质侧链动力学的理解目前受到缺乏分析工具的限制。在这里，我们提出了一种新的分析框架，采用实验性核磁共振（NMR）弛豫测量，结合分子动力学（MD）模拟，以原子分辨率来描述不溶性蛋白质组装体中甲基侧链的详细动力学，使用由朊病毒 HET-s 形成的淀粉样纤维。我们使用 MD 模拟来解释实验结果，其中包括甲基基团旋转和 χ/χ 旋转在内的构象转换跳跃不能用单个相关时间完全描述，而是会采样到一个来自纤维中不断变化的局部结构的广泛相关时间分布。同样，骨架运动也会采样到广泛的相关时间，从 ∼100 ps 到 μs，尽管主要来自不同的动态过程；尽管如此，我们发现骨架与侧链运动没有完全解耦，其中侧链动力学的变化会影响骨架运动，反之亦然。虽然蛋白质组装体中的侧链运动的复杂性使得在实验和模拟之间获得完美一致变得非常具有挑战性，但我们的分析框架提高了对复杂蛋白质组装体的实验动力学测量的解释。
