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Minimal Coarse-Grained Modeling toward Implicit Solvent Simulation of Generic Bolaamphiphiles
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2020-03-30 , DOI: 10.1021/acs.jpcb.0c00734 Somajit Dey 1 , Jayashree Saha 1
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2020-03-30 , DOI: 10.1021/acs.jpcb.0c00734 Somajit Dey 1 , Jayashree Saha 1
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A dual-site dimer model of bola or bipolar amphiphiles is developed based on an earlier single-site model of monopolar amphiphiles [Dey, S.; Saha, J. Phys. Rev. E2017,95, 023315]. This model incorporates both the hydrophobic effect and the hydration force in its anisotropic site–site interactions, thus obviating the need to simulate the water particles explicitly. Such economy of sites and absence of explicit solvents enable molecular dynamics simulations to achieve mesoscopic length and time scales unattainable by any bead-spring model or explicit solvent computations. Our model, however, applies to generic bolas only because the gain in scale can only be obtained by sacrificing the resolution of detailed molecular structures. Thanks to a pivoted dimer architecture, our model can incorporate the essential flexibility of bolas, which leads to their loop or U-shaped conformers. Rigid bolas can also be modeled by the same dimer simply by constraining the rotation about the pivot. Flexible model bolas show fast, spontaneous self-assembly into experimentally observed nanostructures such as micelles and rods. Tightly packed yet fluid monolayers can also be formed from these flexible dimers. Model bolalipids are seen to be less diffusive and produce thicker layers compared to their monopolar counterparts. Bilayers composed of monopolar model lipids show increased stability in the presence of membrane-spanning bolas. Rigid bolas, though achiral themselves, show self-assembly into helical rods. As all these observations agree with well-known characteristics of archaeal lipids and synthetic bolaamphiphiles, our model promises to be useful for mesoscale simulations of bolas in the context of research in lyotropic liquid crystals, biomimetics, drug delivery, and low-molecular-weight hydrogelators.
中文翻译：
通用粗疏两亲分子隐式溶剂模拟的最小粗粒度建模
在较早的单极两亲性单点模型的基础上，开发了双链或双极两亲性双位点二聚体模型[Dey，S.; Saha，J.Phys。Rev E 2017，95 ，023315]。该模型在其各向异性的位点-位点相互作用中兼顾了疏水作用和水合力，因此无需明确模拟水颗粒。这样的位置经济性和不存在显式溶剂，使得分子动力学模拟可以获得任何珠弹簧模型或显式溶剂计算所无法达到的介观长度和时间尺度。但是，我们的模型仅适用于通用玻色子，因为只能通过牺牲详细分子结构的分辨率来获得规模增益。得益于枢轴式二聚体架构，我们的模型可以融合bolas的基本灵活性，从而获得其环状或U形构形。刚体也可以由同一二聚体建模，只需限制围绕枢轴的旋转即可。灵活的模型展示迅速，自发自组装成实验观察到的纳米结构，例如胶束和棒。也可以由这些挠性二聚体形成紧密包装但仍为流体的单层。与单极模型相比，模型玻利班脂扩散性较小，产生的层更厚。由单极性模型脂质组成的双层在存在跨膜的小瓶时显示出增加的稳定性。刚性玻璃瓶，尽管非手性，但显示出自组装成螺旋形杆的能力。由于所有这些观察结果均与古细菌脂质和合成的双亲两亲物的众所周知的特征相吻合，因此我们的模型有望在溶致液晶，仿生药物，药物递送和低分子量水凝胶化剂的研究背景下，对bolas进行中尺度模拟。 。
更新日期：2020-03-30
中文翻译：
通用粗疏两亲分子隐式溶剂模拟的最小粗粒度建模
在较早的单极两亲性单点模型的基础上，开发了双链或双极两亲性双位点二聚体模型[Dey，S.; Saha，J.Phys。Rev E 2017，95 ，023315]。该模型在其各向异性的位点-位点相互作用中兼顾了疏水作用和水合力，因此无需明确模拟水颗粒。这样的位置经济性和不存在显式溶剂，使得分子动力学模拟可以获得任何珠弹簧模型或显式溶剂计算所无法达到的介观长度和时间尺度。但是，我们的模型仅适用于通用玻色子，因为只能通过牺牲详细分子结构的分辨率来获得规模增益。得益于枢轴式二聚体架构，我们的模型可以融合bolas的基本灵活性，从而获得其环状或U形构形。刚体也可以由同一二聚体建模，只需限制围绕枢轴的旋转即可。灵活的模型展示迅速，自发自组装成实验观察到的纳米结构，例如胶束和棒。也可以由这些挠性二聚体形成紧密包装但仍为流体的单层。与单极模型相比，模型玻利班脂扩散性较小，产生的层更厚。由单极性模型脂质组成的双层在存在跨膜的小瓶时显示出增加的稳定性。刚性玻璃瓶，尽管非手性，但显示出自组装成螺旋形杆的能力。由于所有这些观察结果均与古细菌脂质和合成的双亲两亲物的众所周知的特征相吻合，因此我们的模型有望在溶致液晶，仿生药物，药物递送和低分子量水凝胶化剂的研究背景下，对bolas进行中尺度模拟。 。
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