E Van der Giessen

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The tension-driven gating process of MscL from Mycobacterium tuberculosis, Tb-MscL, has been addressed at near-atomic detail using coarse-grained molecular dynamics simulations. To perform the simulations, a novel coarse-grained peptide model based on a thermodynamic parameterization of the amino-acid side chains has been applied. Both the wild-type Tb-MscL(More)
Mechano-sensitive channels are ubiquitous membrane proteins that activate in response to increasing tension in the lipid membrane. They facilitate a sudden, nonselective release of solutes and water that safeguards the integrity of the cell in hypo- or hyper-osmotic shock conditions. We have simulated the rapid release of content from a pressurized liposome(More)
The distribution of disordered proteins (FG-nups) that line the transport channel of the nuclear pore complex (NPC) is investigated by means of coarse-grained molecular dynamics simulations. A one-bead-per-amino-acid model is presented that accounts for the hydrophobic/hydrophilic and electrostatic interactions between different amino acids, polarity of the(More)
Molecular transport across the nuclear envelope in eukaryotic cells is solely controlled by the nuclear pore complex (NPC). The NPC provides two types of nucleocytoplasmic transport: passive diffusion of small molecules and active chaperon-mediated translocation of large molecules. It has been shown that the interaction between intrinsically disordered(More)
Recent studies have revealed the key role of natively unfolded proteins in many important biological processes. In order to study the conformational changes of these proteins, a one-bead-per-amino-acid coarse grained (CG) model is developed, and a method is proposed to extract the potential functions for the local interactions between CG beads.(More)
From a microscopic point of view, the frictional force associated with the relative sliding of rough surfaces originates from deformation of the material in contact, by adhesion in the contact interface or both. We know that plastic deformation at the size scale of micrometres is not only dependent on the size of the contact, but also on the rate of(More)
Influenza viral particles are enveloped by a lipid bilayer. A major step in infection is fusion of the viral and host cellular membranes, a process with large kinetic barriers. Influenza membrane fusion is catalyzed by hemagglutinin (HA), a class I viral fusion protein activated by low pH. The exact nature of the HA conformational changes that deliver the(More)
We report computation results obtained from extensive coarse-grained molecular-dynamics simulations of amorphous ensembles of polymer chains at constant density. In our polymer model, we use bending and torsion potentials acting along the polymer backbone to control the chain stiffness. The static and dynamic properties of the polymer bulk have been(More)
Extensive molecular-dynamics simulations have been performed to study the effect of chain conformational rigidity, controlled by bending and torsion potentials, on self-diffusion in polymer melts. The polymer model employs a novel torsion potential that avoids computational singularities without the need to impose rigid constraints on the bending angles.(More)
We report computation results obtained from extensive molecular dynamics simulations of tensile disentanglement of connector chains placed at the interface between two polymer bulks. Each polymer chain (either belonging to the bulks or being a connector) is treated as a sequence of beads interconnected by springs, using a coarse-grained representation based(More)