Prediction by a neural network of outer membrane β-strand protein topology
Prediction by a neural network of outer membrane β-strand protein topology
复制标题
DOI：
10.1002/pro.5560071119
复制
发表时间：
1998-11-01
期刊：
影响因子：
8
通讯作者：
Breed, J
中科院分区：
文献类型：
--
作者：
Diederichs, K;Freigang, J;Breed, J
训练人工神经网络（NN）以预测细菌外膜（OM）β-链蛋白的拓扑结构。具体而言，NN预测了xy平面中具有外膜的坐标系中Ca原子的z坐标，使得低z值指示周质转角，中等z值指示跨膜β链，并且高z值指示细胞外环。为了获得训练集，将具有已知高分辨率结构的七种OM蛋白（孔蛋白）与它们的孔沿z轴沿着对齐。由此建立了Ca z值与拓扑结构之间的关系。为了预测其他OM蛋白的拓扑结构，所有七种孔蛋白都用于训练集。针对两种迄今为止结构未知的孔蛋白和不属于孔蛋白家族的OM蛋白预测了Z值（拓扑结构），所有这些蛋白与训练集的序列同源性都微不足道。拓扑预测的结果与实验拓扑数据进行了比较。
An artificial neural network (NN) was trained to predict the topology of bacterial outer membrane (OM) beta-strand proteins. Specifically, the NN predicts the z-coordinate of Ca atoms in a coordinate frame with the outer membrane in the xy-plane, such that low z-values indicate periplasmic turns, medium z-values indicate transmembrane beta-strands, and high z-values indicate extracellular loops. To obtain a training set, seven OM proteins (porins) with structures known to high resolution were aligned with their pores along the z-axis. The relationship between Ca z-values and topology was thereby established. To predict the topology of other OM proteins, all seven porins were used for the training set. Z-values (topologies) were predicted for two porins with hitherto unknown structure and for OM proteins not belonging to the porin family, all with insignificant sequence homology to the training set. The results of topology prediction compare favorably with experimental topology data.