Fig. 2. The all-atom structural models of four specific cellular systems.

The conformational dynamics of ligand and receptor in these systems was analyzed by molecular dynamics simulations. The first system is the monomeric receptor TNFR1 on plasma membrane (a). The second system is the membrane-anchored TNFα ligand trimer (b). The third system is the complex formed between soluble ligand trimer and three membrane-bound TNFR1 receptors (sTNFα-TNFR1) (c). Finally, the last system is the complex formed between three membrane-bound TNFR1 receptors and a trimeric ligand TNFα which transmembrane regions are attached to an opposite plasma membrane (mTNFα-TNFR1) (d).