Viral entry begins with the fusion of the viral and host-cell membranes. Type 1 viral membrane fusion is driven by class 1 viral membrane fusion protein, which makes use of its conserved heptad repeats (HR) region to extend its fusion peptide toward the host-cell membrane. The fusion peptide is then embedded in the host-cell membrane. This is followed by refolding of HR region to form a hairpin-like HR region and to bring the viral and host-cell membranes closer for fusion. Type 1 viral membrane fusion is responsible for viral entry of some of the most infectious viruses, SARS-CoV-2, Influenza, and HIV-1. Due to the dynamic nature of this process, it has been challenging to capture the refolding intermediates in atomic resolution via experimental techniques. In this work, we have extensively simulated the HIV-1 gp41 extension and refolding, a class 1 membrane fusion protein, from the pre-fusion to the post-fusion state using simulations of all-atom structure-based models. We show that HR1 of gp41 intrinsically extends beyond 100Å as a three-helical bundle toward the host-cell membrane to reach the pre-hairpin intermediate state that is consistent with a previous cryo-ET experiment. Importantly, we identify the persistent and conserved interactions in gp41 that are important for the refolding of gp41. Based on the pre-hairpin intermediate observed in our simulations, we identify the most exposed stage in the refolding pathway that may exhibit the greatest sensitivity to the membrane-fusion antiviral drugs, T20 and SFT. Our study helps to better understand the mechanism of drug resistance targeting type 1 viral membrane fusion and opens new avenues for therapeutic design.
Unarta et al. (2026) studied this question.