Hepatitis B virus (HBV) infection depends on coordinated capsid assembly and virion production. A hydrophobic pocket at the intradimer interface of the HBV core protein has been linked to secretion phenotypes and shown to bind small molecules, but its interaction landscape remains poorly defined. Here, we combine atomi...
Zixing Fan, Ruo-Qing Jia, Diane L. Lynch et al.· bioRxiv· 0 citations
The outer membrane (OM) of Gram-negative bacteria forms a protective barrier that combines selective permeability with mechanical load-bearing capacity, properties linked to its asymmetric bilayer structure with lipopolysaccharides (LPS) in the outer leaflet and phospholipids (PLs) in the inner leaflet. Unlike most PL...
Jia-Wei Sun, Gvantsa Gutishvili, You He et al.· bioRxiv· 0 citations
This work introduces BEAM, a multiscale framework that learns slow collective variables from coarse-grained simulations to guide all-atom enhanced sampling to explain how vectorial secretion accelerates pertactin folding by excluding an off-pathway kinetic trap.
Lan Yang, Qing Luan, Michael C. Baxa et al.· bioRxiv· 0 citations
Protein structure predictors achieve high single-state accuracy, but it remains unclear whether they can recover functionally relevant conformational ensembles or account for the presence of ligands and/or binding partners. Here, we benchmark AlphaFold3, Boltz-2, Chai-1, and BioEmu on four canonical multi-state protein...
Muhui Ye, Yu-Hong Wang, M. Brogi et al.· bioRxiv· 0 citations
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