Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
+44 1223 790975
ISSN: 0974-276X
+44 1223 790975
Wolfgang B Fischer
National Yang-Ming University, Taiwan
Scientific Tracks Abstracts: J Proteomics Bioinform
A large number of viruses encode small proteins which are expressed in the infected cell to form ion and small molecules conducting channels. These proteins are also called viroporins. For some of the viruses these proteins are essential for infectivity cycle and thus, they comprise interesting drug targets. From the structural and mechanistic point of view, they comprise interesting tools to study membrane protein assembly and dynamics in particular when the outcome of the assembly is an ion conducting system. Computational tools play an important part in this investigation. Using a 2D docking tool structural models of polytopic membrane proteins such as p7 of hepatitis C virus (HCV) with two transmembrane domains (TMDs) and E5 of human papilloma virus �?? 16 (HPV-16) with three TMDs are generated in a putative functional form. From molecular dynamics (MD) simulations of these proteins embedded in a hydrated lipid bilayer ion selectivity of these proteins is investigated also by calculating potential of mean force (PMF) profiles of ions along the conducting pathway. The calculations support weak selectivity of these channel proteins, strengthening the quality of the modeled structures. In addition, full correlation analysis (FCA) provides insight into the dynamic of these proteins. The individual subunits of the protein assemblies show asymmetric behavior during equilibrium dynamics, allowing for proposing several models of gating. Recent Publications 1. Fischer W B, Li L-H, Mahato D R, Wang Y-T and Chen C-P (2014) Viral channel proteins in intracellular protein - protein communication: Vpu of HIV-1, E5 of HPV16 and p7 of HCV. Biochimica et Biophysica Acta 1838:1113-1121. 2. Fischer W B, Kalita M M and Heermann D (2016) Viral Channel forming proteins - how to assemble and depolarize lipid membranes in silico. Biochimica et Biophysica Acta 1858:1710-1721. 3. Y T Wang, R Schilling, R H A Fink and W B Fischer (2014) Ion-dynamics in hepatitis C virus p7 helical transmembrane domains-a molecular dynamics simulation study. Biophysical Chemistry 192:33-40. 4. Mahato D R and Fischer W B (2016) Weak selectivity predicted for modeled bundles of the viral channel forming protein E5 of human papillomavirus-16. Journal of Physical Chemistry B 120:13076-13085. 5. M M Kalita and W B Fischer (2016) Asymmetric dynamics of ion channel forming proteins - hepatitis C virus (HCV) p7 bundles. Biochimica et Biophysica Acta 1858:1462-1470.