Acta Phys. -Chim. Sin. ›› 2011, Vol. 27 ›› Issue (05): 1223-1231.doi: 10.3866/PKU.WHXB20110439

• BIOPHYSICAL CHEMISTRY • Previous Articles     Next Articles

Classification of Coenzyme-A Binding Proteins Based on Co-Factor Binding Modes

FAN Di, LIU Zhen-Ming, JIN Hong-Wei, ZHANG Liang-Ren   

  1. State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
  • Received:2010-12-17 Revised:2011-01-25 Published:2011-04-28
  • Contact: LIU Zhen-Ming, ZHANG Liang-Ren E-mail:liangren@bjmu.eud.cn; zmliu@bjmu.edu.cn
  • Supported by:

    The project was supported by the Major National Science and Technology Program of Key Drug Scheme Funds, China (2009ZX09501-002) and National Natural Science Foundation of China (20802006).

Abstract:

This study developed a mutual recognition of the proteins based on molecular classification, data mining strategies and the statistical clustering method, which was applied to study and classify clusters of coenzyme-A (CoA) binding proteins with their binding patterns extracted by using Pocket1.0 program. Several strategies have been evaluated for the accuracy of the system analysis and the two-step clustering method has been shown to be the best. The results revealed that the known CoA binding proteins can be clustered into three groups by using this approach. The designed classification coefficient was used effectively to identify the critical features for classification. The results show that both hydrogen bonds and hydrophobic interactions are important in all three clusters and that quite a few important residues related to biological activities are involved in the formation of hydrogen bonds. The classification of these interactions and the discovery of the characteristics and differences between the three clusters will have some utility for the design of specific agonists and antagonists.

Key words: Coenzyme-A, Protein classification, Binding mode, Cluster analysis, Pantetheine

MSC2000: 

  • O641