posted on 2024-03-14, 16:12authored byBalázs Fábián, Matti Javanainen
Curved
cellular membranes are both abundant and functionally relevant.
While novel tomography approaches reveal the structural details of
curved membranes, their dynamics pose an experimental challenge. Curvature
especially affects the diffusion of lipids and macromolecules, yet
neither experiments nor continuum models distinguish geometric effects
from those caused by curvature-induced changes in membrane properties.
Molecular simulations could excel here, yet despite community interest
toward curved membranes, tools for their analysis are still lacking.
Here, we satisfy this demand by introducing CurD, our novel and openly available implementation of the Vertex-oriented
Triangle Propagation algorithm to the study of lipid diffusion along
membranes with mean and/or Gaussian curvature. This approach, aided
by our highly optimized implementation, computes geodetic distances
significantly faster than conventional implementations of path-finding
algorithms. Our tool, applied to coarse-grained simulations, allows
for the first time the analysis of curvature effects on diffusion
at size scales relevant to physiological processes such as endocytosis.
Our analyses with different membrane geometries reveal that Gaussian
curvature plays a surprisingly small role on lipid motion, whereas
mean curvature; i.e., the packing of lipid headgroups largely dictates
their mobility.