- Article -
| In Silico Biology 8, 0003 (2007); ©2007, Bioinformation Systems e.V. |
The GTP binding sites interacted with RNA-dependent RNA polymerase of classical swine fever virus in de novo initiation
Zhuofei Xu1,#, Yanjie Chao1,#, Youhui Si1, Jian Wang2, Meilin Jin1, Aizhen Guo1, Ping Qian1, Rui Zhou1 and Huanchun Chen1*
1 The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
2 School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, P. R. China
# These authors contributed equally to the work.
* Corresponding author
Email: hzauvet@public.wh.hb.cn
Edited by H. Michael; received June 15, 2007; revised November 13, 2007; accepted November 14, 2007; published January 05, 2008
Abstract
The NS5B protein of classical swine fever virus (CSFV) is an important enzyme bearing a unique RNA-dependent RNA polymerase (RdRp) activity. The RdRp plays a crucial role in the viral replication cycle and in forming a replicase complex. However, the initiating synthesis mechanism of the CSFV RNA polymerase is unclearly described at present. Our aim is to reveal the RdRp-GTP docking sites and the effective modules of GTP initially bound to the polymerase in starting initiation of replication according to a well predicted CSFV RdRp model. Based on some known crystal structures of RNA polymerase, computational methods were used to establish the model of a CSFV RdRp. An analogous mechanism of CSFV RNA polymerase in de novo initiation was subsequently represented through docking a GTP into the structure model. The unique GTP binding pocket of the polymerase was pointed out: five residues E227, S408, R427, K435, and R439 involved in steady hydrogen bonds and two residues C407 and L232 involved in hydrophobic contact with the GTP. From a genetic evolutionary point of view, three residues C407, S408 and R427 have been suggested to be of particular importance by analysis of residue conservation. It is suggested that these crucial residues should have very significant function in the de novo initiation of the rigorous CSFV polymerase model, which can lead us to design experiments for studying the mechanism of viral replication and develop valid anti-viral drugs.
Keywords: classical swine fever virus, RNA-dependent RNA polymerase, sequence alignment, conservation analysis, GTP docking