Protein Ions Generated by Native Electrospray Ionization: Comparison of Gas Phase, Solution, and Crystal Structures
Protein Ions Generated by Native Electrospray Ionization: Comparison of Gas Phase, Solution, and Crystal Structures
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DOI：
10.1021/acs.jpcb.8b12173
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发表时间：
2019-02-28
影响因子：
3.3
通讯作者：
Konermann, Lars
中科院分区：
文献类型：
--
作者：
Bakhtiari, Maryam;Konermann, Lars
文献中的实验和分子动力学（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结构。然而，这些离子的确切性质仍有待探索。以泛素和溶菌酶为重点，我们考察了几个相关问题。(1)我们采用溶剂MD运行来测试两种蛋白质的x射线结构是否受到晶体填充的影响。主链和侧链取向在溶液中保留，为迄今为止未经审查的依靠晶体数据进行“溶液”与气相比较的方法提供了理由。(2)大多数早期气相蛋白MD研究采用短（ns）模拟窗口。通过将这个时间框架扩展到1 μ s，我们能够观察到泛素中罕见的展开/折叠转变。这些预测波动与离子迁移谱（IMS）检测到的半展开亚群一致。(3)大多数早期的模型研究没有考虑到气态蛋白质中H+的高迁移率。我们首次比较了静态和移动H+模拟，重点关注带正电荷和负电荷的离子。MD运行显示强烈倾向于保留溶液样的骨干折叠，而可滴定/极性侧链塌陷到蛋白质表面。这种侧链坍塌是由分子内盐桥、氢键和电荷偶极子相互作用引起的。我们的研究结果概括了Steinberg等人（ChemBioChem, 2008,9, 2417-2423）的研究结果，他们首先在静态h的短期模拟基础上提出了这种侧链接触的发生。(4)MD构象的碰撞截面计算与IMS实验非常吻合。总的来说，本研究支持这样的观点，即在典型ESI IMS实验的时间尺度上，由于动力学捕获，类溶液蛋白结构可以被保留。
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 mu s, 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.