Department of Chemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada.
J Phys Chem B. 2019 Feb 28;123(8):1784-1796. doi: 10.1021/acs.jpcb.8b12173. Epub 2019 Feb 19.
Experiments and molecular dynamics (MD) simulations in the literature indicate that gaseous proteins generated by electrospray ionization (ESI) can retain native-like structures. However, the exact properties of these ions remain to be explored. Focusing on ubiquitin and lysozyme, we examined several pertinent questions. (1) We applied solvent MD runs to test whether the X-ray structures of both proteins are affected by crystal packing. Main and side-chain orientations were retained in solution, providing a justification for the hitherto unscrutinized approach of relying on crystal data for "solution" versus gas-phase comparisons. (2) Most earlier gas-phase protein MD investigations employed short (ns) simulation windows. By extending this time frame to 1 μs, we were able to observe rare unfolding/folding transitions in ubiquitin. These predicted fluctuations were consistent with a semi-unfolded subpopulation detected by ion mobility spectrometry (IMS). (3) Most earlier modeling studies did not account for the high H mobility in gaseous proteins. For the first time, we compared static and mobile H simulations, focusing on both positively and negatively charged ions. The MD runs revealed a strong preference for retention of a solution-like backbone fold, whereas titratable/polar side chains collapsed onto the protein surface. This side-chain collapse was caused by a multitude of intramolecular salt bridges, H-bonds, and charge-dipole interactions. Our results generalize the findings of Steinberg et al. ( ChemBioChem, 2008, 9, 2417-2423) who had first proposed the occurrence of such side-chain contacts on the basis of short-term simulations with static H. (4) Calculated collision cross sections of the MD conformers were in close agreement with IMS experiments. Overall, this study supports the view that solution-like protein structures can be retained because of kinetic trapping on the time scale of typical ESI-IMS experiments.
实验和文献中的分子动力学（MD）模拟表明，电喷雾电离（ESI）产生的气态蛋白质可以保留天然样结构。然而，这些离子的确切性质仍有待探索。我们以泛素和溶菌酶为研究对象，考察了几个相关问题。（1）我们应用溶剂 MD 模拟来检验这两种蛋白质的 X 射线结构是否受到晶体堆积的影响。在溶液中保留了主链和侧链的取向，为迄今未经审查的方法提供了依据，即依赖晶体数据来比较“溶液”和气相。（2）大多数早期的气相蛋白质 MD 研究采用短（ns）模拟窗口。通过将时间框架延长到 1 μs，我们能够观察到泛素中罕见的展开/折叠转变。这些预测的波动与离子迁移谱（IMS）检测到的半展开亚群一致。（3）大多数早期的建模研究没有考虑气态蛋白质中高 H 迁移率。我们首次比较了静态和动态 H 模拟，重点关注正离子和负离子。MD 模拟揭示了对保留类似溶液的骨架折叠的强烈偏好，而可滴定/极性侧链则折叠到蛋白质表面。这种侧链折叠是由大量的分子内盐桥、氢键和电荷偶极相互作用引起的。我们的结果推广了 Steinberg 等人的研究结果（ChemBioChem，2008，9，2417-2423），他们首次基于静态 H 的短期模拟提出了这种侧链接触的发生。（4）MD 构象的计算碰撞截面与 IMS 实验非常吻合。总的来说，这项研究支持了这样一种观点，即类似溶液的蛋白质结构可以通过在典型 ESI-IMS 实验的时间尺度上的动力学捕获来保留。
