Sequence–function correlation of the transmembrane domains in NS4B of HCV using a computational approach

Ta Chou Huang, Wolfgang B. Fischer*

*此作品的通信作者

研究成果: Article同行評審

摘要

An algorithm is applied to propose a sequence-function correlation of the transmembrane domains (TMDs) of the non-structural protein 4B (NS4B) of hepatitis C virus (HCV). The putative sequence of the TMDs is obtained using 20 available secondary structure prediction programs (SSPPs) with different lengths of the overall amino acid sequence of the protein as input. The results support the notion of four helical TMDs. Whilst the region of the first TMDs leaves room for speculation about an additional TMD, the other three TMDs are consistently predicted. Structural features and the role of each of the TMDs is proposed by applying pairwise sequence alignment using BLAST on the level (i) protein sequence alignment and consequent (ii) function-related alignment. Sequence identity with those TMDs of proteins involved in Ca-homeostasis and generation of replication vesicles, such as Nsp3 of corona viruses, murine coronavirus especially mouse hepatitis virus (MHV), middle east respiratory syndrome coronavirus (MERS), severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2, are suggested. Focusing the search on those proteins in particular and their TMDs playing an active role in their mechanism of function, such as transporters, pumps, viral channel forming protein Vpu of human immunodeficiency virus type 1 (HIV-1) and mediators, suggests TMDs 2 and 4 to have functional roles in NS4B, as well as additionally TMD1 and 3 in case of vesicle formation.

原文English
頁(從 - 到)165-181
頁數17
期刊AIMS Biophysics
7
發行號2
DOIs
出版狀態Published - 2020

指紋

深入研究「Sequence–function correlation of the transmembrane domains in NS4B of HCV using a computational approach」主題。共同形成了獨特的指紋。

引用此