CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model.
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model.
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DOI：
10.1016/j.bpj.2015.10.008
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发表时间：
2015-11
影响因子：
3.4
通讯作者：
Yifei Qi;Xi Cheng;Jumin Lee;J. Vermaas;T. Pogorelov;E. Tajkhorshid;Soohyung Park;Jeffery B. Klauda;W. Im
中科院分区：
文献类型：
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作者：
Yifei Qi;Xi Cheng;Jumin Lee;J. Vermaas;T. Pogorelov;E. Tajkhorshid;Soohyung Park;Jeffery B. Klauda;W. Im
在传统的膜系统的全原子模拟中，脂质的缓慢扩散使得难以对脂质和蛋白质-脂质相互作用的大的重排进行采样。最近，Tajkhorshid和同事开发了高移动的膜模拟物（HMMM）模型，通过用小有机分子代替脂质尾部来加速脂质运动。HMMM模型提供了一个到两个数量级的加速脂质扩散，并且在研究膜-蛋白质缔合中特别有用。然而，建立HMMM模拟系统并不容易，因为它需要对脂质尾部进行复杂的处理。在这项研究中，我们已经开发了CHARMM-GUIHMMM Builder（http：//www.charmm-gui.org/input/hmmm），为用户提供了现成的输入文件，用于模拟有/无蛋白质的HMMM膜系统。模拟各种脂质和蛋白质-脂质系统，以验证HMMM Builder生成的系统的质量，重点是HMMM模型的基本属性和优点。HMMM Builder支持CHARMM-GUI中可用的所有脂质类型，还提供了一个模块，可以在HMMM膜和全长膜之间来回转换。我们希望HMMM Builder能成为研究脂质扩散增强的膜系统的有用工具。
Slow diffusion of the lipids in conventional all-atom simulations of membrane systems makes it difficult to sample large rearrangements of lipids and protein-lipid interactions. Recently, Tajkhorshid and co-workers developed the highly mobile membrane-mimetic (HMMM) model with accelerated lipid motion by replacing the lipid tails with small organic molecules. The HMMM model provides accelerated lipid diffusion by one to two orders of magnitude, and is particularly useful in studying membrane-protein associations. However, building an HMMM simulation system is not easy, as it requires sophisticated treatment of the lipid tails. In this study, we have developed CHARMM-GUIHMMM Builder(http://www.charmm-gui.org/input/hmmm) to provide users with ready-to-go input files for simulating HMMM membrane systems with/without proteins. Various lipid-only and protein-lipid systems are simulated to validate the qualities of the systems generated byHMMM Builderwith focus on the basic properties and advantages of the HMMM model.HMMM Buildersupports all lipid types available in CHARMM-GUI and also provides a module to convert back and forth between an HMMM membrane and a full-length membrane. We expectHMMM Builderto be a useful tool in studying membrane systems with enhanced lipid diffusion.