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Updated: Feb 18, 2026

Subnanometer-resolution Structural Determination of Hemagglutinin from Cryo-electron Tomography of Influenza Viruses
Published on: November 7, 2025
Computation of Hemagglutinin Free Energy Difference by the Confinement Method
Sander Boonstra1, Patrick R Onck1, Erik van der Giessen1
1Micromechanics of Materials, Zernike Institute for Advanced Materials, University of Groningen , 9747 AG Groningen, The Netherlands.
Abstract:
Hemagglutinin (HA) mediates membrane fusion, a crucial step during influenza virus cell entry. How many HAs are needed for this process is still subject to debate. To aid in this discussion, the confinement free energy method was used to calculate the conformational free energy difference between the extended intermediate and postfusion state of HA. Special care was taken to comply with the general guidelines for free energy calculations, thereby obtaining convergence and demonstrating reliability of the results. The energy that one HA trimer contributes to fusion was found to be 34.2 ± 3.4kBT, similar to the known contributions from other fusion proteins. Although computationally expensive, the technique used is a promising tool for the further energetic characterization of fusion protein mechanisms. Knowledge of the energetic contributions per protein, and of conserved residues that are crucial for fusion, aids in the development of fusion inhibitors for antiviral drugs.
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