Chemical Physics Program, University of Maryland, College Park, Maryland, USA.
Biophysics Program, University of Maryland, College Park, Maryland, USA.
Phys Chem Chem Phys. 2023 Apr 12;25(15):10885-10893. doi: 10.1039/d3cp00263b.
Transmembrane helix folding and self-association play important roles in biological signaling and transportation pathways across biomembranes. With molecular simulations, studies to explore the structural biochemistry of this process have been limited to focusing on individual fragments of this process - either helix formation or dimerization. While at an atomistic resolution, it can be prohibitive to access long spatio-temporal scales, at the coarse grained (CG) level, current methods either employ additional constraints to prevent spontaneous unfolding or have a low resolution on sidechain beads that restricts the study of dimer disruption caused by mutations. To address these research gaps, in this work, we apply our recent, in-house developed CG model () to study the folding and dimerization of Glycophorin A (GpA) and its mutants in the presence of Dodecyl-phosphocholine (DPC) micelles. Our results first validate the two-stage model that folding and dimerization are independent events for transmembrane helices and found a positive correlation between helix folding and DPC-peptide contacts. The wild type (WT) GpA is observed to be a right-handed dimer with specific GxxxG contacts, which agrees with experimental findings. Specific point mutations reveal several features responsible for the structural stability of GpA. While the T87L mutant forms anti-parallel dimers due to an absence of T87 interhelical hydrogen bonds, a slight loss in helicity and a hinge-like feature at the GxxxG region develops for the G79L mutant. We note that the local changes in the hydrophobic environment, affected by the point mutation, contribute to the development of this helical bend. This work presents a holistic overview of the structural stability of GpA in a micellar environment, while taking secondary structural fluctuations into account. Moreover, it presents opportunities for applications of computationally efficient CG models to study conformational alterations of transmembrane proteins that have physiological relevance.
跨膜螺旋折叠和自组装在生物信号转导和跨生物膜的运输途径中起着重要作用。通过分子模拟，探索这个过程的结构生物化学的研究一直局限于关注这个过程的单个片段——要么是螺旋形成，要么是二聚化。虽然在原子分辨率下，很难达到长时空尺度，但在粗粒化（CG）水平上，当前的方法要么使用额外的约束来防止自发展开，要么对侧链珠的分辨率较低，这限制了对突变引起的二聚体破坏的研究。为了解决这些研究空白，在这项工作中，我们应用了我们最近开发的 CG 模型（）来研究甘丙肽 A（GpA）及其突变体在十二烷基磷酸胆碱（DPC）胶束中的折叠和二聚化。我们的研究结果首先验证了折叠和二聚化对于跨膜螺旋是独立事件的两阶段模型，并发现了螺旋折叠和 DPC-肽接触之间的正相关关系。野生型（WT）GpA 被观察为右手二聚体，具有特定的 GxxxG 接触，这与实验结果一致。特定的点突变揭示了几个负责 GpA 结构稳定性的特征。虽然由于 T87 缺乏螺旋内氢键，T87L 突变体形成反平行二聚体，但 G79L 突变体的螺旋性略有丧失，并且在 GxxxG 区域形成铰链样特征。我们注意到，由于点突变，疏水环境的局部变化导致了这种螺旋弯曲的发展。这项工作全面概述了 GpA 在胶束环境中的结构稳定性，同时考虑了二级结构的波动。此外，它为应用计算效率高的 CG 模型来研究具有生理相关性的跨膜蛋白的构象改变提供了机会。
