Marc W. van der Kamp

Active site electrostatic effects modulate DBO inhibitor potency against OXA-48 variants

This paper investigates how electrostatic effects in the active site influence the potency of DBO inhibitors against OXA-48 variants using computational simulations.

Rapid classification of β-lactamase activity through AI-based structure prediction and electric field analysis

This study develops a computational method to estimate β-lactamase activity against carbapenems using AI-based structure prediction and electric field analysis, achieving strong correlation with experimental data.

Machine learned potentials with electrostatic embedding accurately capture Kemp eliminase reactivity

The paper trains an ML/MM model to accurately predict reaction barriers in Kemp elimination, capturing experimental differences between designed and evolved enzymes.

Mechanistic origins and evolutionary erosion of collateral sensitivity in a β-lactamase

This paper investigates the molecular mechanisms of collateral sensitivity in β-lactamase evolution, showing how specific mutations alter enzyme structure and drug resistance profiles.

Hydrogen-bonding changes cause differences in imipenem breakdown activity in OXA-48 variants

This study identifies how hydrogen-bonding changes in OXA-48 variants affect imipenem hydrolysis efficiency and resistance.

Acyl-enzyme dynamics, tautomerisation and hydration regulate turnover of carbapenem antibiotics by the OXA-48 β-lactamase

This study investigates how acyl-enzyme tautomerisation, dynamics, and hydration affect carbapenem antibiotic turnover by OXA-48 β-lactamase using X-ray crystallography and molecular dynamics simulations.

Evolution tunes functional sub-state interconversion to boost enzyme function

This paper shows how evolution improves enzyme function by shifting the rate-limiting step from substrate binding to sub-state interconversion in β-lactamase OXA-48.

Correlated dynamics, reactive conformations and non-Arrhenius behaviour in the temperature-dependence of enzyme activity: triosephosphate isomerase

This study investigates the temperature dependence of triosephosphate isomerase activity using experiments and simulations, revealing non-Arrhenius behavior and dynamical differences between enzymes from different organisms.

Influence of Disease-Causing Mutations and Ivacaftor on the Dynamics of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Protein

This study investigates how disease-causing mutations and ivacaftor affect CFTR protein dynamics using molecular simulations and cryo-EM data.

Mechanistic Basis for Inhibition of the Extended Spectrum Class A b-Lactamase GES-1 by Tazobactam and Enmetazobactam

This paper investigates how enmetazobactam and tazobactam inhibit GES-1, an ESBL, revealing structural and mechanistic differences in their acyl-enzyme complexes.

Influence of Wobbling Tryptophan and Mutations on PET Degradation Explored by QM/MM Free Energy Calculations

This study uses QM/MM simulations to analyze PET degradation mechanisms in PET hydrolases, revealing conformational changes and the impact of QM methods on reaction pathways.

Delineation of the Complete Reaction Cycle of a Natural Diels-Alderase

This study provides a molecular description of the complete reaction cycle of the natural Diels-Alderase AbyU using X-ray crystallography, kinetics, and computational simulations.

Variability in mitochondrial import, mitochondrial health and mtDNA copy number using Type II and Type V CRISPR effectors

This study evaluates the effectiveness of different CRISPR effectors for targeting mitochondria, finding that LbCas12a shows better targeting and tolerance than Cas9 variants.