M. McCullagh

Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM

This paper introduces frame-weighted shapeGMM to quantify unbiased biomolecular conformational ensembles from biased simulations, showing improved accuracy in thermodynamic property calculations and structural transitions.

Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase

This study identifies the motif-VI loop as a nucleotide valve in the West Nile Virus NS3 helicase, showing its role in ATP hydrolysis and viral replication through molecular simulations and experimental validation.

The Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13

This paper investigates the ATP hydrolysis and product release mechanism of SARS-CoV-2 NSP13 using molecular dynamics simulations and identifies key residues involved in RNA translocation.

The Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase

This paper models SARS-CoV-2 nsp13 helicase in different substrate states to elucidate its ATP-dependent RNA translocation mechanism using molecular dynamics simulations and structural clustering.

A Hyperactive Kunjin Virus NS3 Helicase Mutant Demonstrates Increased Dissemination and Mortality in Mosquitoes

This study investigates the role of NS3 Motif V mutations in Kunjin virus replication and pathogenesis, finding that S411A mutant increases viral dissemination and mortality in mosquitoes.

Residue-Level Allostery Propagates Through the Effective Coarse-Grained Hessian

This study computes an effective coarse-grained Hessian from molecular dynamics simulations to better understand residue-level allostery in proteins and identifies key residues involved in direct and indirect allosteric pathways.

RNA-dependent structures of the RNA-binding loop in the flavivirus NS3 helicase

This study investigates the RNA-dependent structural dynamics of the flavivirus NS3 helicase RNA-binding loop using molecular dynamics simulations, revealing how RNA binding stabilizes specific conformations and impacts NTPase activity.

Motif V acts as a Regulator of Energy Transduction Between the Flavivirus NS3 ATPase and RNA Binding Cleft

This study investigates the role of Motif V in NS3 helicase energy transduction, finding that mutations increase dsRNA unwinding rates and alter structural communication between ATP and RNA binding sites.