A. J. Pak

Critical Mechanistic Features of HIV-1 Viral Capsid Assembly

This study uses simulations to show IP6 promotes conical HIV-1 capsid formation by stabilizing curvature and shifting assembly kinetics.

Inositol hexakisphosphate (IP6) accelerates immature HIV-1 Gag protein assembly towards kinetically-trapped morphologies

This study uses simulations to show IP6 accelerates HIV-1 Gag assembly, promoting curvature and defects that may aid viral morphogenesis.

Seipin transmembrane segments critically function in triglyceride nucleation and lipid droplet budding from the membrane

This study investigates how seipin's transmembrane segments contribute to triglyceride nucleation and lipid droplet budding using simulations and cell experiments.

Preservation of HIV-1 Gag helical bundle symmetry by bevirimat is central tomaturation inhibition

This study uses molecular dynamics simulations to show that bevirimat's effectiveness against HIV-1 depends on preserving the six-helix bundle symmetry, with escape mutations causing symmetry loss.

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

This study uses coarse-grained models and cryo-ET data to show that SARS-CoV-2 spike trimers cooperatively bind to ACE2 dimers, promoting S1 dissociation and exposing the fusion machinery.

A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

This paper develops a multiscale coarse-grained model of the SARS-CoV-2 virion using structural data and all-atom simulations to enable large-scale viral process simulations.

Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as substrates for proteolytic maturation.

This paper investigates the structure and dynamics of immature HIV-1 Gag lattice edges, revealing partial hexamers and their role in proteolytic maturation.

Membrane-mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins

This study shows lipid clustering stabilizes I-BAR domain aggregates, leading to cylindrical membrane protrusions instead of bulbous ones.

Supercharged Assembly: A Broad-Spectrum Mechanism of Action for Drugs that Undermine Controlled HIV-1 Viral Capsid Formation

This study uses molecular dynamics simulations to show how capsid inhibitors disrupt HIV-1 capsid assembly, leading to structural defects and disassembly, and highlights the importance of dynamic mechanisms in drug design.

Immature HIV-1 Lattice Assembly Dynamics are Regulated by Scaffolding from Nucleic Acid and the Plasma Membrane

This study investigates how HIV-1 Gag polyprotein assembly is regulated by RNA and the plasma membrane using computational and experimental methods, revealing scaffolding roles for these components.