Ligand-receptor dynamics, model

The interaction between ligands and their receptors is clearly a dynamic process. Once the static model of ligand-receptor interaction has been obtained, the stability of ligand-receptor complexes should be evaluated by means of molecular dynamics simulations [18]. 

Once the model of a ligand-receptor complex is built, its stability should be evaluated. Simple molecular mechanics optimization of the putative ligand-receptor complex leads only to the identification of the closest local minimum. However, molecular mechanics optimization of molecules lacks two crucial properties of real molecular systems temperature and, consequently, motion. Molecular dynamics studies the time-dependent evolution of coordinates of complex multimolecular systems as a function of inter- and intramolecular interactions (see Chapter 3). Because simulations are usually performed at nonnal temperature (—300 K), relatively low energy barriers, on the order of kT (0.6 kcal), can... 

E.M. Fallon, D.A. Lauffenburger, Computational model for effects of ligand/receptor binding properties on interleukin-2 trafficking dynamics and T cell proliferation response,... 

Figure 4 illustrates some of the various phenomena that lead to cell migration. Some of these phenomena have been successfiilly formulated into mathematical models of cell migration and are marked with an asterisk in Figure 4. Table II lists some of the most significant models from the literature. These models account for such effects as the population dynamics, the individual cell movements, mechanical force balances between the cell and its substrate, intra-and extrace-llular signaling, and ligand-receptor binding. Other phenomena that are essential to cell migration, such as cytoskeletal rearrangement and focal adhesion formation have not been exhaustively modeled.

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