The extracellular matrix is a complex three-dimensional network of molecules that provides cells with a complex microenvironment. The major constituents of the extracellular matrix such as collagen, elastin and associated proteins form supramolecular assemblies contributing to its physicochemical properties and organization. The structure of proteins and their supramolecular assemblies such as fibrils have been studied at the atomic level (e.g., by X-ray crystallography, Nuclear Magnetic Resonance and cryo-Electron Microscopy) or at the microscopic scale. However, many protein complexes are too large to be studied at the atomic level and too small to be studied by microscopy. Most extracellular matrix components fall into this intermediate scale, so-called the mesoscopic scale, preventing their detailed characterization. Simulation and modelling are some of the few powerful and promising approaches that can deepen our understanding of mesoscale systems. We have developed a set of modelling tools to study the self-organization of the extracellular matrix and large motion of macromolecules at the mesoscale level by taking advantage of the dynamics of articulated rigid bodies as a mean to study a larger range of motions at the cost of atomic resolution.
Keywords: Basement membrane; CG, coarse-grained; Cryo-EM, cryogenic electron microscopy; DOF, degrees of freedom; ECM, extracellular matrix; EGF, epidermal growth factor; Extracellular matrix; FEM, finite element method; MD, molecular dynamics; Mesoscopic scale; Modelling; NC, non-collagenous; NMR, nuclear magnetic resonance; Rigid bodies; SAXS, small-angle X-ray scattering; Simulation.
© 2021 The Author(s).