Biosciences and Biotechnology Division, Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , California 94550 , United States.
Biochemistry and Molecular Biology Department , Georgetown University , Washington , DC 20057 , United States.
J Chem Theory Comput. 2018 Nov 13;14(11):6050-6062. doi: 10.1021/acs.jctc.8b00496. Epub 2018 Oct 10.
Whether lipid rafts are present in the membranes of living cells remains hotly disputed despite their incontrovertible existence in liposomes at 298 K. In attempts to resolve this debate, molecular dynamics (MD) simulations have been extensively used to study lipid phase separation at high resolution. However, computation has been of limited utility in this respect because the experimental distributions of phases in lamellar lipid mixtures are poorly reproduced by simulations. In particular, all-atom (AA) approaches suffer from restrictions on accessible time scales and system sizes whereas the more efficient coarse-grained (CG) force fields remain insufficiently accurate to achieve correspondence with experiment. In this work, we refine the CG Martini parameters for the high- and low-melting temperature ( T) lipids 1,2-dipalmitoyl- sn-glycero-3-phosphatidylcholine (DPPC) and 1,2-dioleoyl- sn-glycero-3-phosphatidylcholine (DOPC). Our approach involves the modification of bonded Martini parameters based on fitting to atomistic simulations conducted with the CHARMM36 lipid force field. The resulting CG parameters reproduce experimental structural and thermodynamic properties of homogeneous lipid membranes while concurrently improving simulation fidelity to experimental phase diagrams of DPPC, DOPC, and cholesterol lipid mixtures. Importantly, the refined parameters provide much better phase accuracy for regions near the critical point that mimic the lipid concentrations under physiological conditions.
尽管脂质筏在 298K 的脂质体中确实存在,但它们是否存在于活细胞的膜中仍然存在争议。为了解决这一争论,人们广泛使用分子动力学(MD)模拟来高分辨率地研究脂质相分离。然而,在这方面,计算的作用有限,因为模拟不能很好地再现层状脂质混合物中各相的实验分布。特别是,全原子(AA)方法受到可访问时间尺度和系统大小的限制,而效率更高的粗粒化(CG)力场仍然不够准确,无法与实验相吻合。在这项工作中,我们改进了用于高低熔点(T)脂质 1,2-二棕榈酰基-sn-甘油-3-磷酸胆碱(DPPC)和 1,2-二油酰基-sn-甘油-3-磷酸胆碱(DOPC)的 CG Martini 参数。我们的方法涉及基于与 CHARMM36 脂质力场进行的原子模拟拟合来修改键合的 Martini 参数。所得的 CG 参数再现了均匀脂质膜的实验结构和热力学性质,同时提高了对 DPPC、DOPC 和胆固醇脂质混合物实验相图的模拟保真度。重要的是,改进后的参数为模拟生理条件下的脂质浓度的临界点附近区域提供了更好的相精度。