B. L. de Groot

Effect Of Two Activators On The Gating Of A K2P Channel

This study uses molecular dynamics simulations to investigate how two activators affect TREK1 channel gating by modulating hydrogen bond networks and carbonyl flipping in the selectivity filter.

Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts

This study determines the structure of AQP0 tetramers in sphingomyelin/cholesterol membranes and shows how cholesterol stabilizes their arrangement through hydrophobic interactions and avidity effects.

Selectivity filter mutations shift ion permeation mechanism in potassium channels

The paper uses molecular dynamics simulations to show that mutations in the selectivity filter of KcsA channels shift the ion permeation mechanism from water-free to co-permeation of K+ and water, reducing conductance and selectivity.

Driving Forces underlying Selectivity Filter Gating in the MthK Potassium Channel

This study investigates selectivity filter gating in the MthK potassium channel and its V55E mutant using electrophysiology and simulations, revealing structural and functional differences compared to KcsA.

Comment on ‘Response to comment on ‘Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size’’

The paper challenges the conclusions of a previous study on box size effects in hemoglobin MD simulations, identifies additional flaws in the response, and reasserts concerns about the validity of the original claims.

Computational Studies of Substrate Transport and Specificity in a Phospholipid Flippase

The paper uses molecular dynamics simulations to study phospholipid transport and specificity in a flippase, revealing a preference for phosphatidylserine and insights into substrate selectivity mechanisms.

The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations

This study evaluates binding free energy calculation methods using the SAMPL6 challenge, finding variations in efficiency and reproducibility across different systems and methods.

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

The paper critiques a study on hemoglobin stability in molecular dynamics simulations, arguing that its findings on box size dependence are not reproducible with more statistics.