P. J. Bond

De-glycosylated non-structural protein 1 enhances dengue virus clearance by limiting PD-L1/PD-1 mediated T cell apoptosis

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.

A coarse-grained model of glycosaminoglycans for biomolecular simulation

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

Impact on S. aureus and E. coli membranes of treatment with chlorhexidine and alcohol solutions: insights from molecular simulations and nuclear magnetic resonance.

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.

A pH-dependent cluster of charges in a conserved cryptic pocket on flaviviral envelopes

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

Mapping the allosteric effects that define functional activity of SARS-CoV-2 specific antibodies

This study identifies site-specific allosteric effects in SARS-CoV-2 Spike protein induced by different neutralizing antibodies, revealing dynamic features that distinguish weak from strong neutralizers.

Viral genome-capsid core senses host environments to prime RNA release

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

SARS-CoV-2 spike protein as a bacterial lipopolysaccharide delivery system in an overzealous inflammatory cascade

This study shows SARS-CoV-2 spike protein binds LPS, which may enhance immune activation via TLR4, with conserved binding sites across variants.

Spike independent infection of human coronavirus 229E in bat cells

This study shows that human coronavirus 229E can infect bat cells without using its spike protein, revealing a spike-independent infection mechanism in bats.

Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein

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.

Site-specific steric control of SARS-CoV-2 spike glycosylation

The paper compares glycosylation patterns of recombinant SARS-CoV-2 spike proteins across labs with infectious virus S protein, finding conserved site-specific glycan maturation stalling linked to protein structure.

The Impact of Gag Non-Cleavage Site Mutations on HIV-1 Viral Fitness from Integrative Modelling and Simulations

This study uses multiscale modelling to show how Gag non-cleavage site mutations affect HIV-1 viral fitness by altering local environments and lipid interactions critical for Gag assembly and protease binding.

Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein

This study uses molecular simulations to uncover how carboxysome shell protein CcmK2 controls molecular permeability through its central pore, validated by experimental mutagenesis.

An alternative HIV-1 non-nucleoside Reverse Transcriptase inhibition mechanism: Targeting the p51 subunit

The paper identifies two chemical scaffolds that inhibit HIV-1 RT by binding to a novel site on the p51 subunit, suggesting a new class of non-nucleoside RT inhibitors.

Extending the Martini coarse-grained forcefield to N-glycans

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.

Molecular Dynamics Simulations of Bacterial Outer Membrane Lipid Extraction: Adequate Sampling?

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

A benzene-mapping approach for uncovering cryptic pockets in membrane-bound proteins

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.

Infectivity of dengue virus serotypes 1 and 2 is correlated to E protein intrinsic dynamics but not to envelope conformations

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.

Molecular basis for the maintenance of lipid asymmetry in the outer membrane of Escherichia coli

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.

Structural basis for endotoxin neutralization and anti-inflammatory activity of thrombin-derived C-terminal peptides

This paper identifies the structural basis of thrombin-derived C-terminal peptides' ability to neutralize endotoxin and reduce inflammation by interacting with LPS and CD14.