解析PDB文件中蛋白质的多聚状态判断方法
本文详细介绍了如何通过PDB文件判断蛋白质的多聚状态（单体、二聚体或四聚体），包括寻找关键线索、分析结晶对称性和可能需要的生物化学实验。提供了一个实用的判断流程，对于分子建模工作至关重要。
Dimer and tetramer are often found in crystal structures and this sometimes confuses many people owing to the crystal symmetry in which the smallest subunit of a protein displays.
Different structrual biologists have different habits: someone will display the whole mutimer in a single PDB file while others prefer to release their structures based on the rule that crystal symmetry contains the smallest subunit of a protein. In this case, a PDB file contains one chain could be a dimer while a PDB file contains multiple chains could also be dimer or even monomer. Now the question is how to judge the protein in a released PDB file is monomer, dimer or tetramer? This questions is of great importance when molecular modeling work is based on such kind of PDB file for different state of protein may lead to different kind of active sites.
The most reliable method is to find clue from raw reference. The PDB creator generally will comment on the bioactivity form of his protein. If this information is not available, we have to analyze the PDB file with displaying symmetry chain nearby manually i.e: checking whether there are lots of H-bond, electronstatic and the like could be found between them or not. Sometimes, it is difficult to decide by this method and in this case it would be necessary to introduce biochemistry experiment.
For more information about symmetry could be found at:
http://en.wikipedia.org/wiki/Crystal_system
http://blog.sciencenet.cn/blog-355217-377795.html
Different structrual biologists have different habits: someone will display the whole mutimer in a single PDB file while others prefer to release their structures based on the rule that crystal symmetry contains the smallest subunit of a protein. In this case, a PDB file contains one chain could be a dimer while a PDB file contains multiple chains could also be dimer or even monomer. Now the question is how to judge the protein in a released PDB file is monomer, dimer or tetramer? This questions is of great importance when molecular modeling work is based on such kind of PDB file for different state of protein may lead to different kind of active sites.
The most reliable method is to find clue from raw reference. The PDB creator generally will comment on the bioactivity form of his protein. If this information is not available, we have to analyze the PDB file with displaying symmetry chain nearby manually i.e: checking whether there are lots of H-bond, electronstatic and the like could be found between them or not. Sometimes, it is difficult to decide by this method and in this case it would be necessary to introduce biochemistry experiment.
For more information about symmetry could be found at:
http://en.wikipedia.org/wiki/Crystal_system
http://blog.sciencenet.cn/blog-355217-377795.html
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