Isolated transmembrane helices arranged across a membrane: computational studies.
Isolated transmembrane helices arranged across a membrane: computational studies.
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跨膜排列的孤立跨膜螺旋：计算研究。
DOI：
10.1093/protein/12.4.305
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发表时间：
1999
期刊：
影响因子：
--
通讯作者：
Nikiforovich,GV
中科院分区：
文献类型：
--
作者：
Tseitin,VM;Nikiforovich,GV
一个计算程序，用于预测一个孤立的螺旋片段跨膜的安排开发。该程序将跨膜螺旋片段放入模型三相系统“水-辛醇-水”中;拉动片段穿过膜，改变其作为刚体的“全局”位置;通过“局部”坐标（侧链的二面角）优化每个全局位置中的螺旋内和溶剂化能量;并选择片段的最低能量全局位置。该程序被应用到45个跨膜螺旋的光合反应中心从绿色红球藻，细胞色素氧化酶从副球菌和细菌视紫红质。在所考虑的三分之二的螺旋片段中，与实验数据相比，该程序预测了片段跨膜的垂直位移，准确度为-0.15 ± 3.12个残基。其余15个片段的准确度为2.17 ± 3.07个残基，约为螺旋转角的一半。该程序预测跨膜螺旋片段的实际膜边界具有更高的精度比现有的统计方法。同时，该过程高估了螺旋片段的倾斜值。
A computational procedure for predicting the arrangement of an isolated helical fragment across a membrane was developed. The procedure places the transmembrane helical segment into a model triple-phase system `water–octanol–water'; pulls the segment through the membrane, varying its `global' position as a rigid body; optimizes the intrahelical and solvation energies in each global position by `local' coordinates (dihedral angles of side chains); and selects the lowest energy global position for the segment. The procedure was applied to 45 transmembrane helices from the photosynthetic reaction center fromRhodopseudomonas viridis, cytochromecoxidase fromParacoccus denitrificansand bacteriorhodopsin. In two thirds of the helical fragments considered, the procedure has predicted the vertical shifts of the fragments across the membrane with an accuracy of –0.15 ± 3.12 residues compared with the experimental data. The accuracy for the remaining 15 fragments was 2.17 ± 3.07 residues, which is about half of a helix turn. The procedure predicts the actual membrane boundaries of transmembrane helical fragments with greater accuracy than existing statistical methods. At the same time, the procedure overestimates the tilt values for the helical fragments.