Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids.
Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids.
复制标题
20 种氨基酸膜渗透的偏压交换元动力学模拟
DOI：
10.3390/ijms19030885
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发表时间：
2018-03-16
影响因子：
5.6
通讯作者：
Zhou Y
中科院分区：
文献类型：
--
作者：
Cao Z;Bian Y;Hu G;Zhao L;Kong Z;Yang Y;Wang J;Zhou Y
氨基酸从水渗透到脂质双分子层的热力学是理解细胞渗透肽机制和膜蛋白结构和稳定性热力学的重要第一步。在这项工作中，我们采用偏压交换元动力学模拟模拟了所有20种氨基酸从水到双棕榈酰磷脂酰胆碱（DPPC）膜（由256种脂质组成）中心的膜渗透，通过定向和扭转角度进行构象采样。我们的结果与以前的实验或计算研究之间存在显著的相关系数（相关系数在0.5-0.6），因此得到的自由能分布的总体准确性得到了支持。自由能谱表明：(1)极性氨基酸比非极性氨基酸具有更大的自由能垒；(2)带负电荷的氨基酸最难进入细胞膜；(3)许多氨基酸在膜穿越过程中的构象转变是降低自由能垒的关键。这些结果代表了第一组模拟所有20种氨基酸的膜交叉自由能谱。
Thermodynamics of the permeation of amino acids from water to lipid bilayers is an important first step for understanding the mechanism of cell-permeating peptides and the thermodynamics of membrane protein structure and stability. In this work, we employed bias-exchange metadynamics simulations to simulate the membrane permeation of all 20 amino acids from water to the center of a dipalmitoylphosphatidylcholine (DPPC) membrane (consists of 256 lipids) by using both directional and torsion angles for conformational sampling. The overall accuracy for the free energy profiles obtained is supported by significant correlation coefficients (correlation coefficient at 0.5–0.6) between our results and previous experimental or computational studies. The free energy profiles indicated that (1) polar amino acids have larger free energy barriers than nonpolar amino acids; (2) negatively charged amino acids are the most difficult to enter into the membrane; and (3) conformational transitions for many amino acids during membrane crossing is the key for reduced free energy barriers. These results represent the first set of simulated free energy profiles of membrane crossing for all 20 amino acids.
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影响因子：
5.5
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
通讯作者：
Lindahl, Erik
DOI：
10.1093/protein/2.3.185
发表时间：
1988-09-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
BIOU, V;GIBRAT, JF;GARNIER, J
通讯作者：
GARNIER, J
影响因子：
6.3
作者：
Giorgino, Toni;Laio, Alessandro;Rodriguez, Alex
通讯作者：
Rodriguez, Alex
影响因子：
3.3
作者：
Ghaemi, Zhaleh;Minozzi, Manuela;Laio, Alessandro
通讯作者：
Laio, Alessandro
影响因子：
5.4
作者：
Almen, Markus Sallman;Nordstrom, Karl J. V.;Schioth, Helgi B.
通讯作者：
Schioth, Helgi B.