a Bioinformatics Programme, Centre for Biological Sciences , Central University of South Bihar , Patna , India.
b Department of Computer Science , Central University of South Bihar , Patna , India.
J Biomol Struct Dyn. 2018 Aug;36(11):2938-2950. doi: 10.1080/07391102.2017.1372311. Epub 2017 Sep 20.
ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known. We hypothesized that the transportation of echonocandinB is mediated via EcdL protein. Henceforth, it is pertinent to know the topological arrangement of TMD0, with other domains of protein and its possible role in transportation of echinocandinB. Absence of effective template for TMD0 domain lead us to model by I-TASSER, further structure has been refined by multiple template modelling using homologous templates of remaining domains (TMD1, NBD1, TMD2, NBD2). The modelled structure has been validated for packing, folding and stereochemical properties. MD simulation for 0.1 μs has been carried out in the biphasic environment for refinement of modelled protein. Non-redundant structures have been excavated by clustering of MD trajectory. The structural alignment of modelled structure has shown Z-score -37.9; 31.6, 31.5 with RMSD; 2.4, 4.2, 4.8 with ABC transporters; PDB ID 4F4C, 4M1 M, 4M2T, respectively, reflecting the correctness of structure. EchinocandinB has been docked to the modelled as well as to the clustered structures, which reveals interaction of echinocandinB with TMD0 and other TM helices in the translocation path build of TMDs.
ATP 结合盒（ABC）转运蛋白在跨膜转运多种生物重要分子方面发挥着广泛的作用。棘白菌素 B（抗真菌）和粗糙脉孢菌 EcdL 蛋白由相同的基因簇编码。EcdL 和棘白菌素 B 的共表达反映了紧密相关的生物学功能。EcdL 属于 ABC 转运蛋白的多药耐药相关蛋白（MRP）亚家族，具有额外的跨膜结构域零（TMD0）。具有原子分辨率的完整 MRP 亚家族结构，包括 TMD0 结构域，尚不清楚。我们假设棘白菌素 B 的转运是通过 EcdL 蛋白介导的。因此，了解 TMD0 与蛋白质其他结构域的拓扑排列及其在棘白菌素 B 转运中的可能作用是很重要的。由于 TMD0 结构域缺乏有效的模板，我们使用 I-TASSER 进行建模，然后使用剩余结构域（TMD1、NBD1、TMD2、NBD2）的同源模板进行多模板建模来进一步完善结构。对模型结构进行了包装、折叠和立体化学性质的验证。在两相环境中进行了 0.1 μs 的 MD 模拟，以完善模型蛋白。通过 MD 轨迹聚类挖掘非冗余结构。模型结构的结构比对显示 Z 分数为-37.9；与 RMSD 的 31.6、31.5；与 ABC 转运蛋白的 31.5、4.2、4.8；PDB ID 分别为 4F4C、4M1M、4M2T，反映了结构的正确性。将棘白菌素 B 对接至模型结构和聚类结构，揭示了棘白菌素 B 与 TMD0 以及跨膜结构域转运通道中其他 TM 螺旋的相互作用。
