The conformational dynamics of Hepatitis C Virus E2 glycoprotein with the increasing number of N-glycosylation unraveled by molecular dynamics simulations

Abstract

The Hepatitis C Virus (HCV), responsible for causing hepatitis and a significant contributor to liver disorders, presents a challenge for treatment due to its high genetic variability. Despite efforts, there is still no effective medication available for this virus. One of the promising targets for drug development involves targeting glycoprotein E2. However, our understanding of the dynamic behavior of E2 and its associated glycans remains limited. In this study, we investigated the dynamic characteristics of E2 with varying degrees of glycosylation using all-atom molecular dynamics simulations. We also explored glycan’s interactions with the protein and among themselves. An overall increase in correlation between the vital protein regions was observed with an increase in glycan number. The protein dynamics is followed by the analysis of glycan dynamics, where the flexibility of the individual glycans was analyzed in their free and bound state, which revealed a decrease in their fluctuation in some cases. Furthermore, we generated the free energy landscape of individual N-glycan linkages in both free and bound states and observed both increases and decreases in flexibility, which can be attributed to the formation and breakage of hydrogen bonds with amino acids. Finally, we found that for a high glycosylation system, glycans interact with glycoprotein and form hydrogen bonds among themselves. Moreover, the hydrogen bond profiles of a given glycan can vary when influenced by other glycans. In summary, our study provides valuable insights into the dynamics of the core region of HCV E2 glycoprotein and its associated glycans.

Communicated by Ramaswamy H. Sarma

Keywords:

• Hepatitis C virus (HCV)
• E2 glycoprotein
• N-glycans
• molecular dynamics
• conformational dynamics

Data availability statement

The data supporting this study’s findings are available from the corresponding author (PK) upon reasonable request.

Disclosure statement

The authors declare no potential conflict of interest.

Ethics statement

There is no human or animal experiment in this study.

Additional information

Funding

This work was supported by the Department of Science and Technology, Govt. of India (grant number ECR/2017/000010 and DST/NSM/R&D_HPC_Applications/2021/03.18). The funding organization has not played any role in designing the study and manuscript preparation.