J. R. Perilla

Elasticity of the HIV-1 Core Facilitates Nuclear Entry and Infection

This study shows that HIV-1 core elasticity is essential for nuclear entry and infection, with capsid-targeting drugs reducing elasticity and impairing infectivity.

The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir

This paper identifies the mechanism of resistance to the HIV-1 integrase inhibitor pirmitegravir and develops a more potent analog to overcome this resistance.

Molecular architecture and conservation of an immature human endogenous retrovirus

The paper determines the structure of immature HERV-K VLPs using cryoET STA, revealing conserved assembly mechanisms across retroviruses.

Structural Basis of HIV-1 Maturation Inhibitor Binding and Activity

This study determines the structural basis of HIV-1 maturation inhibitor binding and resistance using NMR, revealing an allosteric mechanism and conformational changes in SP1 variants.

Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining

This paper introduces a transferable coarse graining method using unsupervised machine learning to create accurate coarse molecules for biomolecular simulations, demonstrating its effectiveness across various systems.

Equilibrium dynamics of the pre- and post-cleavage regions of SP1 are separately shifted by the HIV-1 maturation inhibitor Bevirimat

This study uses molecular simulations to show that bevirimat and IP6 bind to HIV-1 immature lattice without cooperativity and reveal independent dynamics of SP1 regions.

HIV-1 Mutants that Escape the Cytotoxic T-Lymphocytes are Defective in Viral DNA Integration

This study shows that an HIV-1 mutation escaping CTL response impairs viral DNA integration, and compensatory mutations or host factors can rescue this defect.

Full scale structural, mechanical and dynamical properties of HIV-1 liposomes.

This study uses molecular dynamics simulations to analyze the structural, mechanical, and dynamical properties of HIV-1 liposomes and their relationship to lipid composition.

Curvature of the retroviral capsid assembly is modulated by a molecular switch

The paper identifies key residues that enable a molecular switch in retroviral capsid proteins, allowing curvature changes during capsid assembly.

Scalable Analysis of Authentic Viral Envelopeson FRONTERA

The paper uses molecular dynamics simulations on the Frontera supercomputer to analyze authentic viral envelopes at large scale, providing insights into viral infection mechanisms.

A DNA-origami nuclear pore mimic reveals nuclear entry mechanisms of HIV-1 capsid

This study uses DNA-origami NPC mimics to show HIV-1 capsid uses a trimeric interface and RRR motif to pass through nuclear pores, bypassing the FG motif of NUP153.

Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis

This study investigates how HIV-1 capsid permeability to metabolites affects dNTP import and reverse transcription, revealing a mechanism involving IP6 and BHC.

Accelerating Prediction of Chemical Shift of Protein Structures on GPUs

The paper accelerates chemical shift prediction for large protein complexes using GPU acceleration, reducing computation time from 14 hours to 46.71 seconds.

High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein cavities

The paper introduces a 3D ray casting method to classify space inside and outside biomolecular containers, enabling efficient analysis of small-molecule transport, lipid diffusion, and protein cavities in molecular dynamics simulations.

MxB restricts HIV-1 by targeting the tri-hexamer interface of the viral capsid

This paper identifies the molecular mechanism by which MxB restricts HIV-1 by binding to the tri-hexamer interface of the viral capsid.