A brief history of visualizing membrane systems in molecular dynamics simulations

Abstract

Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.

The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes

“…75 It cannot be understated how beneficial and exciting sophisticated visualizations and animated graphics have become, catalyzing the understanding and interpretation of complex membrane systems. 76 This is especially true for the qualitative and quantitative analysis of: lipid diffusion and fluidity; 77 membrane packing defects; 78 and lipid domain phase separations. 15,79 Furthermore, there is a diverse range of computational techniques that enable the exploration of realistic simulations of biological membrane curvature and shapes known to be linked to many cellular functions.…”

From complex data to clear insights: visualizing molecular dynamics trajectories

“…In this report, we aim to study the visual representation approaches and metaphors that can be used to visualize large scale molecular dynamics simulations, taking advantage of the graphic and technological developments briefly mentioned in this section. A recent perspective article discussed similar aspects in the particular context of membrane systems, and we refer the interested reader to this work (Corey et al, 2023). In our review, we will prioritize areas not discussed in the more specialized perspective provided by Corey et al…”

“…Literature on coarse-graining approaches is abundant. We will here only skim over a handful of articles that give some thought to the visualization aspects and have not been discussed in ( Corey et al, 2023 ), where coarse-graining is very frequent. SIRAH ( Machado and Pantano, 2016 ; Klein et al, 2023 ) comprises a set of utilities that includes the conversion of all-atom coordinates to arbitrary residue-based CG schemes and features a VMD plugin designed for visualizing, analyzing, and extracting pseudo-atomistic details from coarse-grained trajectories conducted using the SIRAH force field.…”