Rotamers and Swapaa Virtual Mutation

Rotamers is an interface for showing amino acid sidechain rotamers and optionally replacing the original sidechain, also implemented as the swapaa command. The rotamers can be shown all at once, as in the figure, or individually by choosing rows in the dialog.

The figure shows binding-site residues of the thyroid hormone receptor β with hormone bound, PDB 3gws. Rotamers for the hormone-resistance mutations N331H and L346R are shown as partially transparent sticks, with H-bonds (light blue dashed line) and clashes (light purple dashed lines) calculated for the histidine rotamers at position 331. The rotamer-list dialog for this position is also shown. Command script rotamers.cxc contains the initial, noninteractive part of the setup.

These mutations are described in Cardoso et al., Endocrine (2020). Although one histidine rotamer may be able to form the same pocket-stabilizing H-bond as the wild-type asparagine, it also clashes with several atoms (third row in the dialog). H-bonds and clashes are not shown for the arginine rotamers at 346, but they all clash significantly with the hormone and/or other pocket atoms.

Calmodulin and Target Peptide

Calmodulin (CaM) acts as a calcium sensor. When its four Ca++ sites are fully occupied, it binds and modulates the activity of various downstream proteins, including CaM-dependent protein kinase I (CaMKI). Here, a complex between CaM and its target peptide from CaMKI (PDB 1mxe) is shown with cartoons, a transparent molecular surface, silhouette outlines, and light soft ambient occlusion. (If you prefer a less smudgy/rustic appearance, try using light gentle instead.) For image setup other than positioning, see the command file cam.cxc.

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