Melo M N, Ingólfsson H I, Marrink S J
Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
J Chem Phys. 2015 Dec 28;143(24):243152. doi: 10.1063/1.4937783.
Sterols play an essential role in modulating bilayer structure and dynamics. Coarse-grained molecular dynamics parameters for cholesterol and related molecules are available for the Martini force field and have been successfully used in multiple lipid bilayer studies. In this work, we focus on the use of virtual sites as a means of increasing the stability of cholesterol and cholesterol-like structures. We improve and extend the Martini parameterization of sterols in four different ways: 1-the cholesterol parameters were adapted to make use of virtual interaction sites, which markedly improves numerical stability; 2-cholesterol parameters were also modified to address reported shortcomings in reproducing correct lipid phase behavior in mixed membranes; 3-parameters for ergosterol were created and adapted from cholesterols; and 4-parameters for the hopanoid class of bacterial polycyclic molecules were created, namely, for hopane, diploptene, bacteriohopanetetrol, and for their polycyclic base structure.
甾醇在调节双层结构和动力学方面起着至关重要的作用。胆固醇及相关分子的粗粒度分子动力学参数可用于Martini力场，并已成功应用于多个脂质双层研究中。在这项工作中，我们专注于使用虚拟位点来提高胆固醇和类胆固醇结构的稳定性。我们通过四种不同方式改进并扩展了甾醇的Martini参数化：1-调整胆固醇参数以利用虚拟相互作用位点，这显著提高了数值稳定性；2-修改胆固醇参数以解决在混合膜中再现正确脂质相行为方面报告的缺点；3-从胆固醇创建并调整了麦角固醇的参数；4-创建了细菌多环分子类藿烷类的参数，即对于藿烷、双萜烯、细菌藿四醇及其多环基本结构。
