Conformational Equilibria of Multimodal Chromatography Ligands in Water and Bound to Protein Surfaces
Conformational Equilibria of Multimodal Chromatography Ligands in Water and Bound to Protein Surfaces
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水中和蛋白质表面结合的多模式色谱配体的构象平衡
DOI：
10.1021/acs.jpcb.9b01218
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Garde, Shekhar
中科院分区：
文献类型：
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作者：
Bilodeau, Camille L.;Lau, Edmond Y.;Cramer, Steven M.;Garde, Shekhar
多模式色谱使用具有多种相互作用模式的小配体，例如，带电荷的、疏水的或氢键的，以从复杂的混合物中分离蛋白质。预期多模式配体与蛋白质相互作用的机制受到配体构象等因素的影响。在这里，我们研究了两个商业上使用的多模式阳离子交换配体，Capto MMC和Nuvia cPrime，在一系列溶剂，Lennard-Jones（LJ）液体，乙醇和水的构象平衡，使用分子动力学（MD）模拟。通过将配体构象映射到这些溶剂以及低和高介电介质中的两个关键扭转角ω和φ上，我们量化了分子内和溶剂介导的相互作用的相对重要性。在高介电介质中，Capto MMC优先对三种构象进行采样，这些构象通过分子内扭转势（ω上）和LJ相互作用的组合来稳定。在LJ液体中，溶剂分子与分子内相互作用竞争，同时提供渗透力，稳定配体位点之间的较近和较远距离。这具有使构象景观“变平”的总体效果。有趣的是，在乙醇和水中，酰胺氢和溶剂分子之间的氢键稳定了Capto MMC的两种额外构象，其中ω呈现不太有利的顺式构型。配体在游离溶液中与三种治疗性抗体片段的MD模拟显示，配体构象平衡在与蛋白质结合时保持有效不变。尽管在结合时总配体有20-30%的脱水，但氢键结合位点的脱水程度要小得多，特别是在顺式样构型中。Nuvia cPrime的构象偏好与Capto MMC相似，除了不存在烷基硫醇尾引起的对称性效应。表征这两个配体在自由溶液中的构象平衡，并绑定到蛋白质提供了一个基础，为开发一个机制的理解蛋白质多模式配体相互作用。
Multimodal chromatography uses small ligands with multiple modes of interaction, e.g., charged, hydrophobic or hydrogen bonding, to separate proteins from complex mixtures. The mechanism by which multimodal ligands interact with proteins is expected to be affected by ligand conformations, among other factors. Here, we study conformational equilibria of two commercially used multimodal cation exchange ligands, Capto MMC and Nuvia cPrime, in a range of solvents, a Lennard-Jones (LJ) liquid, ethanol, and water, using molecular dynamics (MD) simulations. By mapping ligand conformations onto two key torsion angles, ω and φ, in these solvents and in low and high dielectric media, we quantify the relative importance of intramolecular and solvent-mediated interactions. In a high dielectric medium, Capto MMC preferentially samples three conformations, which are stabilized by a combination of an intramolecular torsion potential (on ω) and LJ interactions. In an LJ liquid, solvent molecules compete with intramolecular interactions while simultaneously providing an osmotic force, stabilizing both closer and farther distances between ligand sites. This has the overall effect of “flattening out” the conformational landscape. Interestingly, in ethanol and water, hydrogen bonding between the amide hydrogen and solvent molecules stabilizes two additional conformations of Capto MMC in which ω takes on less favorable cis-like configurations. MD simulations of ligands in free solution with three therapeutic antibody fragments show that ligand conformational equilibria remain effectively unchanged upon binding to proteins. Although, there is 20–30% dehydration of the overall ligand upon binding, the hydrogen-bonding sites are dehydrated to a much smaller extent, particularly in cis-like configurations. Conformational preferences of Nuvia cPrime are similar to that of Capto MMC, except for the effect of symmetry arising from the absence of an alkyl thiol tail. Characterizing the conformational equilibria of these two ligands in free solution and bound to a protein provides a foundation for developing a mechanistic understanding of protein–multimodal ligand interactions.