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.

The architecture of the human ribosome has been determined at near-atomic resolution by electron microscopy (Anger et al., Nature 497:80 (2013)). The structure, comprising 82 proteins and five RNA molecules, is shown with shadows cast from all directions to accentuate depth. In the background are schematic representations of contacts between the component molecules.

See the image setup script card.cxc using the 'Tis the Season color palette (credit to MrsP). See also the RBVI holiday card gallery.

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