{Reference Type}: Journal Article
{Title}: Dynamic framework for large-scale modeling of membranes and peripheral proteins.
{Author}: Sadeghi M;Rosenberger D;
{Journal}: Methods Enzymol
{Volume}: 701
{Issue}: 0
{Year}: 2024
{Factor}: 1.682
{DOI}: 10.1016/bs.mie.2024.03.018
{Abstract}: In this chapter, we present a novel computational framework to study the dynamic behavior of extensive membrane systems, potentially in interaction with peripheral proteins, as an alternative to conventional simulation methods. The framework effectively describes the complex dynamics in protein-membrane systems in a mesoscopic particle-based setup. Furthermore, leveraging the hydrodynamic coupling between the membrane and its surrounding solvent, the coarse-grained model grounds its dynamics in macroscopic kinetic properties such as viscosity and diffusion coefficients, marrying the advantages of continuum- and particle-based approaches. We introduce the theoretical background and the parameter-space optimization method in a step-by-step fashion, present the hydrodynamic coupling method in detail, and demonstrate the application of the model at each stage through illuminating examples. We believe this modeling framework to hold great potential for simulating membrane and protein systems at biological spatiotemporal scales, and offer substantial flexibility for further development and parametrization.