Author

James C. Gumbart

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Open access Sep 2026

Independent tuning of outer membrane fluidity and mechanics in Gram-negative bacteria

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

#protein folding Open access Aug 2026

Autotransporter folding avoids a kinetic trap during vectorial translocation across the bacterial outer membrane

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

Open access Jul 2026

Benchmarking AI Protein Structure Predictors Reveals a Persistent Bias in Multi-State Proteins

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