Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States.
Department of Chemical Engineering , University of Washington , 105 Benson Hall, Box 351750 , Seattle , Washington 98195-1750 , United States.
J Phys Chem B. 2019 Dec 26;123(51):10915-10929. doi: 10.1021/acs.jpcb.9b09245. Epub 2019 Dec 16.
Interpreting dynamics in solid-state molecular systems requires characterization of the potentially heterogeneous environmental contexts of molecules. In particular, the analysis of solid-state nuclear magnetic resonance (ssNMR) data to elucidate molecular dynamics (MD) involves modeling the restriction to overall tumbling by neighbors, as well as the concentrations of water and buffer. In this exploration of the factors that influence motion, we utilize atomistic MD trajectories of peptide aggregates with varying hydration to mimic an amorphous solid-state environment and predict ssNMR relaxation rates. We also account for spin diffusion in multiply spin-labeled (up to 19 nuclei) residues, with several models of dipolar-coupling networks. The framework serves as a general approach to determine essential spin couplings affecting relaxation, benchmark MD force fields, and reveal the hydration dependence of dynamics in a crowded environment. We demonstrate the methodology on a previously characterized amphiphilic 14-residue lysine-leucine repeat peptide, LKα14 (Ac-LKKLLKLLKKLLKL-c), which has an α-helical secondary structure and putatively forms leucine-burying tetramers in the solid state. We measure the R relaxation rates of uniformly C-labeled and site-specific H-labeled leucines in the hydrophobic core of LKα14 at multiple hydration levels. Studies of 9 and 18 tetramer bundles reveal the following: (a) for the incoherent component of C relaxation, the nearest-neighbor spin interactions dominate, while the H-H interactions have minimal impact; (b) the AMBER ff14SB dihedral barriers for the leucine C-C bond ("methyl rotation barriers") must be lowered by a factor of 0.7 to better match the H data; (c) proton-driven spin diffusion explains some of the discrepancy between experimental and simulated rates for the C and C nuclei; and (d) C relaxation rates are mostly underestimated in the MD simulations at all hydrations, and the discrepancies identify likely motions missing in the 50 ns MD trajectories.
解析固态分子体系中的动力学需要对分子所处的潜在非均相环境进行特征描述。特别是，通过对固态核磁共振（ssNMR）数据进行分析以阐明分子动力学（MD），需要对分子受到相邻分子的整体限制以及水和缓冲液浓度进行建模。在对影响分子运动的因素的探索中，我们利用具有不同水合作用的肽聚集的原子模拟 MD 轨迹来模拟非晶态固态环境并预测 ssNMR 弛豫率。我们还考虑了多自旋标记（多达 19 个核）残基中的自旋扩散，使用了几种偶极耦合网络模型。该框架可作为一种通用方法，用于确定影响弛豫的基本自旋耦合、基准 MD 力场，并揭示在拥挤环境中动力学的水合依赖性。我们在先前表征的两亲性 14 残基赖氨酸-亮氨酸重复肽 LKα14（Ac-LKKLLKLLKKLLKL-c）上展示了该方法，该肽具有α-螺旋二级结构，并且在固态中可能形成亮氨酸掩埋四聚体。我们在多个水合水平下测量了 LKα14 疏水区中均 C 标记和位点特异性 H 标记亮氨酸的 R1 弛豫率。对 9 和 18 个四聚体束的研究揭示了以下几点：（a）对于 C 弛豫的非相干分量，最近邻自旋相互作用占主导地位，而 H-H 相互作用的影响最小；（b）必须将亮氨酸 C-C 键的 AMBER ff14SB 二面角势垒（“甲基旋转势垒”）降低 0.7 倍，才能更好地匹配 H 数据；（c）质子驱动的自旋扩散可以解释实验和模拟速率之间的一些差异；（d）在所有水合作用下，MD 模拟中 C 弛豫速率都被大大低估了，并且这些差异确定了在 50 ns MD 轨迹中可能缺失的运动。
