Postsynaptic signal transduction and dynamics of protein solutions
Postsynaptic signal transduction plays a crucial role in brain functioning. It consists of molecular signalling cascades, initiated at the postsynaptic membrane, where hundreds of different bio - macromolecules are diffusing and interacting. To date, the spatio-temporal correlations between the various types of membrane proteins and lipids are still largely unexplored even in the initial stage of signalling. We have developed a mesoscale protein - membrane - cytosol model of initial - stage postsynaptic signalling which we analyze using multiparticle collision dynamics (MPC) and Langevin dynamics simulation methods. Realistic input parameters are obtained from quasi - atomistic simulations performed in our collaborating group at INM-9 (V. Calandrini / P. Carloni). This allows to bridge the gap between molecular and mesoscale length and time scales. We currently explore how effective interactions, diffusion and possible clustering (oligomer formation) of specific GPCR proteins are influenced by the membrane and surrounding cytosol fluid.
In a related project, using MPC simulations and theory we study the phase behavior and dynamics of interacting globular proteins confined to quasi-two-dimensional (Q2D) motion along a planar fluid interface embedded in a bulk fluid. We consider proteins with competing short - range attractive and long - range repulsive interactions which exhibit a plethora of equilibrium and non - equilibrium cluster phases. The interplay of Q2D protein motion and solvent - mediated hydrodynamic interactions gives rise to peculiar effects such as anomaloulsly enhanced collective diffusion down a concentration gradient.
- Theory and mesoscale computer simulation of biological soft matter (proteins, membranes, charge-stabilized colloids, microgels).
- Structure, dynamics and phase behavior in bulk and under quasi-two-dimensional confinement.
- Filtration modelling.
- Postsynaptic signal transduction (mesoscale simulations in a project jointly with INM-9).
Prof. Dr. Gerhard Naegele
Building 04.6 / Room 106
Hydrodynamics of immiscible binary fluids with viscosity contrast: A multiparticle collision dynamics approach,
Z. Tan, V. Calandrini, J.K.G. Dhont, G. Nägele and R.G. Winkler, Soft Matter 17, 7978 (2021).
Clustering and dynamics of particles in dispersions with competing interactions: Theory and simulation,
S. Das, J. Riest, R.G. Winkler, G. Gompper, J.K.G. Dhont and G. Nägele, Soft Matter 14, 91 (2018).
Dynamics of suspensions of hydrodynamically structured particles: Analytic theory and applications to experiments, J. Riest, T. Eckert, W. Richtering and G. Nägele, Soft Matter 11, 2821 (2015).
Viscosity and diffusion: Crowding and salt effects in protein solutions,
M. Heinen, F. Zanini, F. Roosen-Runge, D. Fedunova, F. Zhang, M. Hennig, T. Seydel, R. Schweins, M. Sztucki, M. Antalik, F. Schreiber and G. Nägele, Soft Matter 8, 1404 (2012).
Long-time dynamics of concentrated charge-stabilized colloids,
P. Holmqvist and G. Nägele, Phys. Rev. Lett. 104, 058301(2010).