2Danalysis: A toolbox for analysis of lipid membranes and biopolymers in two-dimensional space
Molecular simulations expand our ability to learn about the interplay of biomolecules. Biological membranes, composed of diverse lipids with varying physicochemical properties, are highly dynamic environments involved in cellular functions. Proteins, nucleic acids, glycans and bio-compatible polymers are the machinery of cellular processes both in the cytosol and at the lipid membrane interface. Lipid species directly modulate membrane properties, and affect the interaction and function of other biomolecules. Natural molecular diffusion results in changes of local lipid distribution, affecting the membrane properties. Projecting biophysical and structural membrane and biopolymer properties to a two-dimensional plane can be beneficial to quantify molecular signatures in a reduced dimensional space to identify relevant interactions at the interface of interest, i.e. the membrane surface or biopolymer-surface interface. Here, we present a toolbox designed to project membrane and biopolymer properties to a two-dimensional plane to characterize patterns of interaction and spatial correlations between lipid-lipid and lipid-biopolymer interfaces. The toolbox contains two hubs implemented using MDAKits architecture, one for membranes and one for biopolymers, that can be used independently or together. Three case studies demonstrate the versatility of the toolbox with detailed tutorials in GitHub. The toolbox and tutorials will be periodically updated with other functionalities and resolutions to expand our understanding of the structure-function relationship of biomolecules in two-dimensions. SIGNIFICANCE2Danalysis is a significant contribution for the systematic analysis of membrane and biopolymers simulations at planar interfaces. Developed under the open-source MDAKit framework, it enables efficient analysis of trajectories and provides versatile tools for projecting biophysical properties onto a two-dimensional plane. These capabilities enhance the visualization of spatial and temporal changes in membrane characteristics, such as order parameters, and support the study of biopolymer-surface interactions by analyzing adsorption and confinement mechanisms at 2D interfaces. The users can customize the toolbox to study complex 2D phenomena from molecular simulation.