A. J. Mulholland

This paper uses D-NEMD simulations to study how the fatty acid site in the glycosylated SARS-CoV-2 spike modulates its structure and function, revealing allosteric networks and the role of glycans.

The paper investigates how electric fields in class A β-lactamases influence carbapenemase activity using molecular dynamics simulations and identifies key positions that correlate with enzyme efficiency.

The paper uses four in silico methods to analyze allostery in K-Ras4B, showing how different 'languages' of allostery change with GTP perturbation.

This study investigates the temperature dependence of enzyme catalysis by analyzing MalL and its mutants, showing cooperative conformational transitions and introducing models to explain non-Arrhenius behavior.

This study shows that epistasis in enzyme evolution arises from shifting the rate-limiting step in the catalytic cycle, leading to substantial activity enhancements through synergistic mutations.

This study develops a thermostable ADDomer-based nanoparticle vaccine that neutralizes SARS-CoV-2 and cross-reacts with VOCs, demonstrating its potential for nasal administration.

The paper uses D-NEMD simulations to identify allosteric sites and resistance-associated networks in SARS-CoV-2 Mpro.

This study identifies how tautomer-specific deacylation and {Omega}-loop flexibility enable KPC-2 β-lactamase to efficiently hydrolyze carbapenems, revealing structural and energetic mechanisms for its broad-spectrum activity.

This study uses molecular dynamics simulations to analyze sequence variations in SARS-CoV-2 spike proteins and their effects on receptor binding domain interfaces, fatty acid binding, and furin cleavage site motions across variants.

This study compares how SARS-CoV-2 spike variants respond to linoleic acid removal using simulations, finding significant differences in allosteric connections that may affect transmissibility and virulence.

This study uses molecular dynamics simulations to analyze how full and partial agonists induce different conformational changes in the α4β2 nicotinic acetylcholine receptor, affecting signal propagation.

This study uses molecular dynamics simulations to show that the fatty acid binding site in the SARS-CoV-2 spike protein influences distant functional regions and variant behavior.

This study investigates the mechanism by which TMPyP4 induces unfolding of RNA G-quadruplexes using simulations and experiments, revealing a two-state interaction mechanism.

This study shows that increasing rigidity in a de novo peroxidase enhances its activity but alters its temperature dependence, resembling natural enzymes.

This study identifies allosteric communication pathways in Class A β-lactamases using molecular dynamics simulations, showing how amino acid substitutions affect enzyme activity and antibiotic resistance.

This study shows that directed evolution of a designer enzyme introduces dynamical changes that increase activation heat capacity and nonlinearity in temperature dependence through correlated dynamical networks.

The paper uses molecular simulations to show that the SARS-CoV-2 spike protein's Y674-R685 loop binds to nicotinic acetylcholine receptors, with specific interactions and conformational changes observed across different receptor subtypes.

The paper uses experiments and simulations to show that heat capacity changes in enzyme-catalyzed reactions can be predicted by molecular dynamics simulations, revealing dynamic changes beyond the active site.