Computationally modelled structure of type IV pilus PilA of Aggregatibacter actinomycetemcomitans

Some bacterial type IV pili structures have been determined with Cryo-EM, X-ray diffraction or similar method. The type IVa pilus PilA of Aggregatibacter actinomycetemcomitans, an oral pathogen, shares sequence identity with other bacterial type IVa pili. To understand the structure of AaPilA at the molecular level, we performed computational modeling studies. To model the filament, we utilized the GalaxyGemini web server using different monomer conformations from molecular dynamics simulations as a seed; then, we extended the structure to 14-mer by employing the cryo-EM map file of type IV pilus from enterohemorrhagic E. coli. The structures were predicted for a full-length monomer PilA_D7S, N-terminally truncated monomer PilA_D7S_Δ1-27 and 14-homo-oligomer PilA_D7S_14mer. PilAD7S_Δ1-27 and PilAD7S share the same secondary structural elements: an N-terminal α-helix, four antiparallel β-strands, a hypervariable segment and a flexible C-terminus. The homo-oligomeric PilAD7S from our comp...已有部分细菌IV型菌毛结构通过冷冻电镜（Cryo-EM）、X射线衍射（X-ray diffraction）或类似方法完成解析。作为一种口腔致病菌，伴放线聚集杆菌（Aggregatibacter actinomycetemcomitans）的IVa型菌毛蛋白PilA，与其他细菌IVa型菌毛存在序列同源性。为在分子层面解析AaPilA的结构，本研究开展了计算建模相关研究。在长丝建模环节，我们依托GalaxyGemini在线服务器，以分子动力学模拟得到的不同单体构象作为初始种子；随后，以肠出血性大肠杆菌（enterohemorrhagic E. coli）IV型菌毛的冷冻电镜密度图文件为模板，将结构延伸为14聚体。本研究分别对全长单体PilA_D7S、N端截短单体PilA_D7S_Δ1-27以及14聚同源寡聚体PilA_D7S_14mer进行了结构预测。PilA_D7S_Δ1-27与PilA_D7S拥有一致的二级结构元件：N端α螺旋、四条反向平行β链、一个高变区段以及一段柔性C端。本研究得到的同源寡聚化PilA_D7S结构……