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Simulations |
Knottins are small but structurally well-defined proteins. They are well suited for theoretical studies, e.g. molecular dynamics simulations. Prediction and characterization of the native state of cyclic knottinsA new computational method, NcCYP, has been proposed to predict the native state conformational ensemble of cyclic disulfide-rich miniproteins from sequence. The method does not assume any specific disulfide bond pairing. A hierarchical multi-resolution exploration is used that provides a large number of independent conformations. [Shehu et al., 2008]. Molecular dynamics simulations and MM-PBSA free energies of disulfide-rich miniproteins with unconventional disulfide connectivitiesUnconventional connectivities were reported for the knottin kalata B1 and for two scorpion toxins, maurotoxin and spinoxin. Molecular dynamics simulations and MM-PBSA free energy estimations suggest that these unconventional connectivities do not correspond to the lowest free energy minimum. The unconventional maurotoxin structure might arise from a kinetically controlled folding process. [Combelles et al., 2008]. Molecular dynamics simulationsA molecular dynamics simulation protocol has been devised that is able to refold the knottin PCI (Potato Carboxypeptidase Inhibitor) from unfolded species. The method was also used to predict the structure of PCI samples with non-native disulfide bridges. [Marti-Renom et al., 1998; Marti-Renom et al., 2000]. |