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Correlation between Protein Sequence Similarity and Crystallization Reagents in the Biological Macromolecule Crystallization Database
Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, Shaanxi, China
Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an 710072, Shaanxi, China
* Author to whom correspondence should be addressed.
Received: 1 June 2012; in revised form: 9 July 2012 / Accepted: 10 July 2012 / Published: 27 July 2012
Abstract: The protein structural entries grew far slower than the sequence entries. This is partly due to the bottleneck in obtaining diffraction quality protein crystals for structural determination using X-ray crystallography. The first step to achieve protein crystallization is to find out suitable chemical reagents. However, it is not an easy task. Exhausting trial and error tests of numerous combinations of different reagents mixed with the protein solution are usually necessary to screen out the pursuing crystallization conditions. Therefore, any attempts to help find suitable reagents for protein crystallization are helpful. In this paper, an analysis of the relationship between the protein sequence similarity and the crystallization reagents according to the information from the existing databases is presented. We extracted information of reagents and sequences from the Biological Macromolecule Crystallization Database (BMCD) and the Protein Data Bank (PDB) database, classified the proteins into different clusters according to the sequence similarity, and statistically analyzed the relationship between the sequence similarity and the crystallization reagents. The results showed that there is a pronounced positive correlation between them. Therefore, according to the correlation, prediction of feasible chemical reagents that are suitable to be used in crystallization screens for a specific protein is possible.
Keywords: crystallization reagents; protein sequence similarity; protein crystallization; molecular structure; X-ray crystallography
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MDPI and ACS Style
Lu, H.-M.; Yin, D.-C.; Liu, Y.-M.; Guo, W.-H.; Zhou, R.-B. Correlation between Protein Sequence Similarity and Crystallization Reagents in the Biological Macromolecule Crystallization Database. Int. J. Mol. Sci. 2012, 13, 9514-9526.
Lu H-M, Yin D-C, Liu Y-M, Guo W-H, Zhou R-B. Correlation between Protein Sequence Similarity and Crystallization Reagents in the Biological Macromolecule Crystallization Database. International Journal of Molecular Sciences. 2012; 13(8):9514-9526.
Lu, Hui-Meng; Yin, Da-Chuan; Liu, Yong-Ming; Guo, Wei-Hong; Zhou, Ren-Bin. 2012. "Correlation between Protein Sequence Similarity and Crystallization Reagents in the Biological Macromolecule Crystallization Database." Int. J. Mol. Sci. 13, no. 8: 9514-9526.