P. M. Kasson

Structural prediction of chimeric immunogens to elicit targeted antibodies against betacoronaviruses

The paper designs chimeric spike proteins to elicit targeted antibodies against betacoronaviruses using AlphaFold and molecular dynamics, achieving 5/7 accurate predictions.

The ACE-2 receptor accelerates but is not biochemically required for SARS-CoV-2 membrane fusion.

This study shows that ACE-2 accelerates but is not required for SARS-CoV-2 membrane fusion when an alternative attachment factor is present.

Influenza virus membrane fusion is promoted by the endosome-resident phospholipid bis(monoacylglycero)phosphate

This study shows that BMP enhances influenza virus fusion efficiency but not kinetics, suggesting it may be a general co-factor for endosomal viral entry.

Simulation-guided engineering of antibiotics for improved bacterial uptake

This study develops physics-based methods to predict and optimize antibiotic uptake in Gram-negative bacteria, showing strong correlation with experimental data and antimicrobial activity.

Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms

The paper uses molecular dynamics simulations to show influenza hemagglutinin drives fusion via two sequential intramembrane mechanisms: lipid tail protrusion/stalk formation and distal leaflet engagement/curvature.

Hybrid refinement of heterogeneous conformational ensembles using spectroscopic data

This study develops a method to refine heterogeneous conformational ensembles using spectroscopic data, showing improved accuracy in capturing conformational states of syntaxin-1a.

Detecting and controlling dye effects in single-virus fusion experiments

The paper shows fluorescent dyes can alter viral membrane fusion efficiency and kinetics, and provides a method to minimize these effects.

gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations

The paper introduces a Python API for GROMACS that enables custom potential functions and efficient simulation ensembles without modifying the core code.