J. K. Marzinek

This study shows that de-glycosylation of N207 in DENV NS1 reduces viral fitness and enhances clearance by limiting PD-L1/PD-1 mediated T cell apoptosis.

This paper develops a coarse-grained model for glycosaminoglycans compatible with Martini forcefields, enabling simulation of their conformational and thermodynamic properties.

This study uses molecular simulations and NMR to examine how chlorhexidine and alcohol affect S. aureus and E. coli membranes, showing chlorhexidine's role in membrane partitioning.

This paper identifies a pH-dependent charge cluster in flaviviral envelope proteins that influences domain dissociation and fusion through molecular dynamics simulations.

This study identifies how viral RNA interacts with coat proteins to sense host environments and trigger capsid disassembly in Turnip crinkle virus.

This study identifies a novel cryptic pocket on the SARS-CoV-2 spike protein using molecular dynamics simulations and validates its druggable potential through experimental methods.

This paper extends the Martini forcefield to model N-glycans by optimizing coarse-grained parameters and validating them against experimental data on lectin binding and solvation properties.

This study evaluates simulation protocols for accurately sampling lipopolysaccharide dynamics in bacterial membranes, finding that decoupling cations improves convergence while lateral mixing remains slow.

The paper introduces a benzene-mapping method using MD simulations to identify cryptic pockets in membrane-bound proteins, revealing a druggable pocket in the dengue virus E protein.

This study investigates the relationship between dengue virus serotypes 1 and 2 infectivity and the dynamics of their envelope proteins, finding that intrinsic dynamics, not envelope conformations, correlate with infectivity.

The paper defines the molecular architecture of the OmpC-MlaA complex in E. coli and shows how it transports phospholipids across the outer membrane to maintain lipid asymmetry.