Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface

Abstract

Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles.

Advanced Hepatitis C Virus Replication PDE Models within a Realistic Intracellular Geometric Environment

“…Section 2.2), labeled for the ER surface (calnexin marker) and for the MWs (dsRNA marker). Based on these z-stacks, we used the reconstructed various realistic ER surfaces as described previously [35,36,37] with the aid of NeuRA2 [35,36,46,47]. (For a brief overview over the reconstruction procedure, we refer to Appendix H.)…”

“…However, due to a lack of adequate parameters for the diffusion–reaction equations, the model is more qualitative than quantitative. Therefore, we also built up a modeling framework to estimate the diffusion constant of the HCV NS5A viral protein on the ER surface [35,36,37]. Overall, our previous work on modeling the HCV RNA replication cycle [34] and first spatial parameter estimation [35,36,37] are likely the first attempts in the literature to establish a fully spatiotemporally resolved biophysical description of virus dynamics at an intracellular level.…”

Special Issue “Mathematical Modeling of Viral Infections”

“…This issue on mathematical modelling of viral infections covers a number of viruses: HCV [ 12 , 13 , 14 , 15 ], hepatitis B virus (HBV) [ 16 , 17 ], HIV [ 18 ], influenza [ 19 ], and even viruses that are used to combat cancer [ 20 ]. Moreover some of the modelling, although applied to specific diseases, has wider applications as they describe intracellular processes that are common to a number of infections [ 12 , 13 , 14 ]. Bingham et al provide a description of the viral encapsidation process mediated by packaging signalling (PS) motifs, how this can result in a measure of viral fitness dependent on how well this packaging occurs, and then assess how targeting these conserved regions of the viral genome could produce HCV therapies that are less susceptible to viral escape than current direct acting agents [ 14 ].…”

“…Bingham et al provide a description of the viral encapsidation process mediated by packaging signalling (PS) motifs, how this can result in a measure of viral fitness dependent on how well this packaging occurs, and then assess how targeting these conserved regions of the viral genome could produce HCV therapies that are less susceptible to viral escape than current direct acting agents [ 14 ]. The two works by Knodel and collaborators describe intracellular dynamics of HCV proteins and viral RNA over the endoplasmic reticulum (ER) and membranous webs within the cytoplasm [ 12 , 13 ], which will have wider application to other infections that use similar pathways for viral replication, assembly and export (potentially other Flaviviridae such as West Nile Virus, Dengue virus, and Zika virus).…”

“…These have the advantage of a more straightforward implementation within numerical software, as well as requiring fewer parameters than agent-based models. For situations when both space and time elements are needed, such as in the work describing viral protein movement within HCV-infected hepatocytes [ 12 , 13 ], partial differential equations (PDEs) are the natural setting (to see how complex these dynamics can be and the geometry that can be incorporated into these models, the reader is directed to the movies in the Supplementary Material for these articles). Finally, where mutations must be tracked as is the case for the evolution of a viral quasi-species [ 14 ], a stochastic system of equations is necessary.…”