TRAF2 Docking with Related Proteins <i>in Silico</i> Studies

Zeng, Fanlong; Wu, Q.; Guo, E.; Guo, H.; Wang, H.; Shan, J.; Wei, R.

doi:10.14712/fb2012058010016

Folia Biologica > Archive > 2012, Vol. 58 > Issue 1 > TRAF2 Docking with Related Proteins…

Fol. Biol. 2012, 58, 16-23

https://doi.org/10.14712/fb2012058010016

TRAF2 Docking with Related Proteins in Silico Studies

Fanlong Zeng¹, Q. Wu², E. Guo¹, H. Guo¹, H. Wang¹, J. Shan¹, R. Wei¹

¹Department of Medical Biology, Hubei University of Medicine, Hubei, PRC
²Department of Otolaryngology, Taihe Hospital, Shiyan, Hubei, PRC

Received June 2011
Accepted November 2011

Using the protein-protein docking program, this study investigates the relationship between TRAF2 and its related proteins and the diversity within the 3D structures of TRAF2s. TRAF2 exists in monomer, trimer, and hexamer forms and it can combine with a number of proteins. Through comparative analysis we found that TRAF2(122), TRAF2(22), TRAF2(21740), TRAF2(2), TRAF2(22ABC), and TRAF2(Phyre) perform very close homoousia in docking with the same group of ligands, though these TRAF2s come from different sources. The TRAF2-related proteins of cluster 1 change docking values strongly from top to bottom. The TRAF2related proteins of clusters 2 and 3 have acceptable variation of the docking values. In consideration of the amino acid percentage, TRAF2-related proteins of cluster 2 represent appropriate docking values.