- Last Updated: Wednesday, 21 August 2013 11:40
Although secondary structure changes of proteins can not be modelled in Martini, tertiary conformational changes are unrestricted and in principle realistic within the general approximations underlying the coarse-grained model.
A fine example is the gating process of the mechano-sensitive channel of large conductance, MscL. Both the wild-type Tb-MscL and its gain-of-function mutant V21D embedded in a solvated lipid bilayer have been simulated . Putting the membrane under tension, the channels undergo significant conformational changes in accordance with an iris-like expansion mechanism, reaching a conducting state on a microsecond timescale. The most pronounced expansion of the pore has been observed for the V21D mutant, which is consistent with the experimentally shown gain-of-function phenotype of the V21D mutant. Due to the inhomogeneous pressure distribution around the protein , the mere shape change of the channel provides a large contribution to the gating energy . The gating of a MscL channel embedded in a liposome has also been simulated  (see figure). Other channel proteins that have been simulated with Martini include voltage-gated potassium channels  and the SecY channel .
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