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made with VMD
One of life's great achievements is the development and maintenance of multi-cellular organisms, from an embryo to adulthood. Multitudes of cells need to be sorted and resorted into tissues, organs, and body of living beings. One strategy towards this end is to endow cells with so-called adhesion proteins that connect a mechanical framework inside cells through the cell membrane with other cells. A key type of adhesion protein is cadherin (calcium-dependent adherent protein) that stretches through the cell surface five-tandem domains. The outermost domain can stick to a cadherin molecule from an adjacent cell. Crystallography provided the molecular structures of cadherin pairs and resolved in atomic detail the cadherin-cadherin contact between cells. This prompted a collaboration that aimed at probing the adhesion strength of cadherin pairs through steered molecular dynamics simulations stretching the pairs apart. Results of the simulations were reported in a recent publication that employed NAMD as well as VMD. As shown by crystallography, the cadherins each insert a tryptophan residue into the other protein. The link thereby established can be broken only through strong forces that induce a step-wise slippage of the residues first out of their binding pockets and then along the protein surface. This scenario suggests a mechanism for selectivity among cadherins, i.e., why among the various cadherins found on the surfaces of cells some adhere much better to each other than others.