Toward a Designable Extracellular Matrix: Molecular Dynamics Simulations of an Engineered Laminin-Mimetic, Elastin-Like Fusion Protein
Toward a Designable Extracellular Matrix: Molecular Dynamics Simulations of an Engineered Laminin-Mimetic, Elastin-Like Fusion Protein
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走向可设计的细胞外基质：工程层粘连蛋白模拟、弹性蛋白样融合蛋白的分子动力学模拟
DOI：
10.1021/acs.biomac.6b00951
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发表时间：
2016
影响因子：
6.2
通讯作者：
Lampe, Kyle J.
中科院分区：
文献类型：
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作者：
Tang, James D.;McAnany, Charles E.;Mura, Cameron;Lampe, Kyle J.
天然细胞外基质（ECM）表现出特定基质蛋白和其他组织成分之间的分子相互作用网络。在这些自然自组装超分子系统的指导下，我们设计了一种基质衍生的蛋白质嵌合体，该嵌合体包含与弹性蛋白样多肽（ELP）融合的层粘连蛋白球状（LG）结构域。这种二分设计提供了一个灵活的蛋白质工程平台：（i）层粘连蛋白是人脑和其他神经组织中ECM的关键多功能组分，使其成为我们融合的理想生物活性组分，以及（ii）已知在体内耐受良好的ELP提供了具有可调物理化学（粘弹性，温敏性）特性的自组装支架。新蛋白质的实验表征是资源密集型的，在实验室中检查许多可能的设计将是一个巨大的挑战。计算方法提供了一个前进的方向：分子动力学（MD）模拟可以用来分析候选LG-ELP融合蛋白的结构/物理行为，特别是在构象特性方面突出我们的设计目标，如组装倾向的温度范围内跨越逆温度转变。作为检查模型LG-ELP融合蛋白的物理特性（包括其温度依赖性结构行为）的第一步，我们在生理相关温度（290-320 K）范围内模拟了蛋白质。我们发现，ELP区，建立在原型（VPGXG）5支架，是相当灵活的，并有一个倾向，β丰富的二级结构接近生理（310-315 K）温度。我们的轨迹表明，温度依赖性埋葬的疏水补丁在ELP区域，耦合到当地的水结构动力学和介导的脂肪族侧链之间的分子内接触，与温度相关的结构转变在已知的ELP聚合物。由于ELP片段压缩成富含β的结构和该区域的不同溶剂化性质之间的联系，我们认为ELP序列和组成的未来变化可用于系统地改变相变曲线，从而改变我们的LG-ELP融合蛋白系统的一般功能。
Native extracellular matrices (ECMs) exhibit networks of molecular interactions between specific matrix proteins and other tissue components. Guided by these naturally self-assembling supramolecular systems, we have designed a matrix-derived protein chimera that contains a laminin globular-like (LG) domain fused to an elastin-like polypeptide (ELP). This bipartite design offers a flexible protein engineering platform: (i) laminin is a key multifunctional component of the ECM in human brains and other neural tissues, making it an ideal bioactive component of our fusion, and (ii) ELPs, known to be well-tolerated in vivo, provide a self-assembly scaffold with tunable physicochemical (viscoelastic, thermoresponsive) properties. Experimental characterization of novel proteins is resource-intensive, and examining many conceivable designs would be a formidable challenge in the laboratory. Computational approaches offer a way forward: molecular dynamics (MD) simulations can be used to analyze the structural/physical behavior of candidate LG-ELP fusion proteins, particularly in terms of conformational properties salient to our design goals, such as assembly propensity in a temperature range spanning the inverse temperature transition. As a first step in examining the physical characteristics of a model LG-ELP fusion protein, including its temperature-dependent structural behavior, we simulated the protein over a range of physiologically relevant temperatures (290–320 K). We find that the ELP region, built upon the archetypal (VPGXG)5scaffold, is quite flexible and has a propensity for β-rich secondary structures near physiological (310–315 K) temperatures. Our trajectories indicate that the temperature-dependent burial of hydrophobic patches in the ELP region, coupled to the local water structure dynamics and mediated by intramolecular contacts between aliphatic side chains, correlates with the temperature-dependent structural transitions in known ELP polymers. Because of the link between compaction of ELP segments into β-rich structures and differential solvation properties of this region, we posit that future variation of ELP sequence and composition can be used to systematically alter the phase transition profiles and, thus, the general functionality of our LG-ELP fusion protein system.