James C. Gumbart

This study shows that outer membrane fluidity and mechanics in Gram-negative bacteria can be independently controlled by altering lipid composition and crosslinking.

The paper explains how autotransporter proteins avoid a kinetic trap during secretion by using a computational framework to reveal hidden conformational states.

The paper identifies ligands that bind beyond a known hydrophobic pocket at the HBV core protein interface using molecular dynamics and fragment mapping.

This study benchmarks AI protein structure predictors on multi-state proteins, revealing persistent biases in capturing conformational ensembles and ligand interactions.

The paper models and validates the coordination mechanism between PilT and PilU ATPases during type IV pilus retraction using AlphaFold 3 and molecular dynamics simulations.

This study investigates the biogenesis of the SARS-CoV-2 M protein, revealing key steps in its insertion, folding, and oligomerization.

DeepPath predicts protein transition pathways using physics-based deep learning, achieving accurate results faster than molecular dynamics simulations.

The paper uses Weighted Ensemble simulations to study Hepatitis B virus capsid assembly, revealing new conformations and modulator effects not accessible via standard MD simulations.

The paper presents a 3.3 Å cryo-EM map of Vibrio cholerae competence pilus and a full-length pseudoatomic model of the CPM, revealing unique structural features and mechanical properties.

This paper uses machine learning to classify molecular dynamics simulations of viral capsid assembly intermediates, distinguishing between apo and CAM-bound states with high accuracy.

This study investigates how mRNA structures affect ribosome intersubunit rotation using smFRET and MD simulations.

The paper investigates how Mg2+ and pH regulate the structural dynamics of AcrA in the AcrAB-TolC multidrug efflux pump, showing Mg2+ maintains structural mobility for optimal pump function across varying environments.

This study shows that OMVs with different O-antigen lengths induce similar protection against Salmonella infections, and boosting enhances cross-protection.

The paper compares glycosylation and structural changes between SARS-CoV-2 Omicron and D614G spike proteins, finding increased surface accessibility in Omicron due to altered glycosylation.

This study defines the substrate recognition mechanism of Doa10 using structural and functional analyses in yeast, revealing a lateral tunnel and fence-like domains that facilitate substrate access.

The paper shows that phosphorylation of the yeast Gγ subunit Ste18 at multiple sites modulates its structure and affects MAPK activation.

The paper uses molecular dynamics simulations to study HBV capsid assembly modulators, identifying structures that predict assembly outcomes and discovering compounds with anti-viral activity.