Sheehan David, O'Sullivan Siobhán
Proteomics Research Group, Department of Biochemistry, University College Cork, Lee Maltings, Prospect Row, Mardyke, Cork, Ireland.
Bioeng Bugs. 2011 Nov-Dec;2(6):299-305. doi: 10.4161/bbug.2.6.16116. Epub 2011 Nov 1.
For even the best-studied species, there is a large gap in their representation in the protein databank (PDB) compared to within sequence databases. Typically, less than 2% of sequences are represented in the PDB. This is partly due to the considerable experimental challenge and manual inputs required to solve three dimensional structures by methods such as X-ray diffraction and multi-dimensional nuclear magnetic resonance (NMR) spectroscopy in comparison to high-throughput sequencing. This gap is made even wider by the high level of redundancy within the PDB and under-representation of some protein categories such as membrane-associated proteins which comprise approximately 25% of proteins encoded in genomes. A traditional route to closing the sequence-structure gap is offered by homology modelling whereby the sequence of a target protein is modelled on a template represented in the PDB using in silico energy minimisation approaches. More recently, online homology servers have become available which automatically generate models from proffered sequences. However, many online servers give little indication of the structural plausibility of the generated model. In this paper, the online homology server Geno3D will be described. This server uses similar software to that used in modelling structures during structure determination and thus generates data allowing determination of the structural plausibility of models. For illustration, modelling of a chemotaxis protein (CheY) from Pseudomononas entomophila L48 (accession YP_609298) on a template (PDB id. 1mvo), the phosphorylation domain of an outer membrane protein PhoP from Bacillus subtilis, will be described.
即使是研究得最透彻的物种，其在蛋白质数据库（PDB）中的代表性与序列数据库相比仍存在很大差距。通常，PDB中所呈现的序列不到2%。部分原因在于，与高通量测序相比，通过X射线衍射和多维核磁共振（NMR）光谱等方法解析三维结构需要相当大的实验挑战和人工投入。PDB内部的高度冗余以及某些蛋白质类别（如膜相关蛋白，约占基因组编码蛋白质的25%）的代表性不足，使得这一差距进一步扩大。同源建模提供了一种缩小序列 - 结构差距的传统方法，即使用计算机能量最小化方法，根据PDB中呈现的模板对目标蛋白质的序列进行建模。最近，在线同源服务器已经出现，它们可以根据提供的序列自动生成模型。然而，许多在线服务器几乎没有给出所生成模型结构合理性的任何指示。在本文中，将介绍在线同源服务器Geno3D。该服务器使用与结构测定过程中建模结构所用的类似软件，因此生成的数据能够确定模型的结构合理性。为了说明这一点，将描述以枯草芽孢杆菌外膜蛋白PhoP的磷酸化结构域（PDB编号1mvo）为模板，对嗜虫假单胞菌L48的趋化蛋白（CheY，登录号YP_609298）进行建模的过程。
