Publications by Denis Bucher | EPFL Graph Search

Insight into Lipopolysaccharide Translocation by Cryo-EM structures of a LptDE Transporter in Complex with Pro-Macrobodies

Henning Paul-Julius Stahlberg, Dongchun Ni, Iwan Zimmermann, Denis Bucher

2021

Coordination Numbers of K+ and Na+ Ions Inside the Selectivity Filter of the KcsA Potassium Channel: Insights from First Principles Molecular Dynamics

Ursula Röthlisberger, Denis Bucher, Leonardo Guidoni, Paolo Carloni

Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K+ and Na+ ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K+ ions were found to displa ...

Elsevier2010

Molecular simulations of ion channels: a quantum chemist's perspective

Ursula Röthlisberger, Denis Bucher

Rockefeller University Press2010

Developing Improved Charge Sets for the Modeling of the KcsA K+ Channel Using QM/MM Electrostatic Potentials

Ursula Röthlisberger, Denis Bucher, Leonardo Guidoni

The performance of popular molecular mechanics (MM) force fields in treating problems that involve ion-channel interactions is explored. We have used quantum mechanical/molecular mechanical (QM/MM) calculations to compute the electrostatic potential inside ...

2009

The protonation state of of the Glu-71/Asp-80 residues in the KcsA Potassium channel: A first-principles QM/MM molecular dynamics study

Ursula Röthlisberger, Denis Bucher, Leonardo Guidoni

2007

Tools to study molecules in high electric fields : ab-initio molecular dynamics studies of selectivity in a potassium channel and the catalytic efficiency of a DNA repair enzyme

Denis Bucher

This thesis describes the application of the quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello methodology to two systems of high biological interest: (a) The potassium channel KcsA from Streptomyces lividans and (b) The DNA repair enzyme EndoIV ...

EPFL2006