Acta Phys. -Chim. Sin. ›› 2011, Vol. 27 ›› Issue (10): 2447-2456.doi: 10.3866/PKU.WHXB20111009

• BIOPHYSICAL CHEMISTRY • Previous Articles     Next Articles

Statistical Coupling Analysis of a SH3 Domain Sequence Set

XU Hai-Song, LI Xiao-Qin, ZENG Yi   

  1. School of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
  • Received:2011-04-19 Revised:2011-07-26 Published:2011-09-27
  • Contact: LI Xiao-Qin E-mail:lxq0811@bjut.edu.cn
  • Supported by:

    The project was supported by the Beijing Municipal Natural Science Foundation, China (4092008, 4112010).

Abstract: Given the long range correlation characteristics of information about protein foldability and thermostability the multiple sequence alignment of a SH3 domain was analyzed using the modified statistical coupling analysis (SCA) method. Results show that the statistically conserved energy from the SCA method could be used to evaluate the site conservation of the SH3 sequence set properly. Sites with a high average coupling energy correspond to structurally and functionally important positions. Perturbing analysis on several sites revealed local and nonlocal perturbing modes in the SH3 domain. By combining the SCA and the clustering reorder method the structural core and the non-structural core sites of the SH3 domain, and detailed differences between several functional sites could be distinguished. Different perturbing modes that involve different sites exist in the SH3 domain. By sharing the common perturbing sites and the responding sites, different perturbing modes can interact. The coupling responding mode of all the sites in the structure was thus determined. Coupling information about the SH3 domain can improve our understanding about the relationship between the protein sequence and its structure as well as its function. It is also valuable in new protein design.

Key words: Protein function, Protein stability, Perturbing mode, Coupling responding mode, Residue coevolution

MSC2000: 

  • O641