Multiscale modelling of the extracellular matrix

Abstract

Highlights We introduce a set of theoretical modelling tools based on rigid body dynamics. Basement membrane components are modelled as articulated chains of rigid bodies. User-defined constraints can be used to investigate and modulate self-assembly. Sampled conformations can be exported to all-atom representation.

UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape

“…To our knowledge, there is no other generally applicable interactive method for this purpose. In certain specific cases, such interactive simulations have been explored, e.g., for the extracellular matrix [ 58 ]. We consider them extremely valuable for hypothesis generation and exploratory evaluation of a system at the beginning of a new project.…”

“…Another exciting possibility is exploring the potential for advanced multiscale modeling based on membrane shape. A multiscale setup for this model could allow for the inclusion of diffusion within the membrane plane, as Wong has already demonstrated with a coarser shape-based rather than atom-based model to represent an extracellular matrix patch [ 58 , 59 ]. With UNILIPID, such a membrane embedding could be achieved at the bead level down to atomic precision and combined with lattice Boltzmann approaches, as we have explored in our work with Dry Opep [ 60 ].…”

Estudo dos efeitos da instilação nasal de colágeno tipo V na inflamação e remodelamento pulmonar na DPOC experimental

“…A MEC é uma rede tridimensional complexa de macromoléculas, que não apenas fornece o arcabouço estrutural físico em que as células se inserem, mas também regula muitos processos celulares incluindo crescimento, migração, diferenciação, sobrevivência, homeostase e morfogênese 104 Entre as macromoléculas do parênquima pulmonar estão o colágeno, elastina, proteoglicanos, glicosaminoglicanos (GAGs) e glicoproteínas de adesão, que se distribuem em meio aquoso, determinando as propriedades mecânicas do tecido pulmonar. Os GAGs e proteoglicanos formam uma substância hidratada tipo gel, que é altamente resistente a forças compressivas.…”