Mutating Residues

A common task when working with proteins is to mutate residues. There are multiple ways of doing this with Maestro, from simple single substitutions to complex jobs that evaluate the effects of mutation on structural stability or binding. For the simple mutations, you may want to minimize the residue and its neighbors afterward. The various ways of mutating residues are summarized below.

To mutate residues to a particular residue type:

  1. Select the residue(s) in the Workspace.

  2. Right-click on the selection and choose Mutate Residue.

  3. In the residue selector:

    • For proteins, choose from 20 standard and 10 variant residues.
    • For DNA or RNA, choose from the 4 standard residues, or choose DNA/RNA Nucleotide to mutate a DNA nucleotide to an RNA nucleotide, or an RNA nucleotide to a DNA nucleotide, depending on which residue type is currently selected.
    • To mutate to nonstandard residues, click Nonstandard Residues at the bottom of the residue selector to open the Mutate to Nonstandard Residues Dialog Box.

To mutate a residue to multiple residue types, as new structures:

  1. click the Tasks button and browse to Protein Preparation and Refinement → Mutate Residues.
  2. Pick a residue in the Workspace that you want to mutate.
  3. Select the residue types you want to mutate to.
  4. Click Mutate.

One entry is created for each mutation, with a title that describes the mutation.

You can mutate residues by editing the side chains with the 3D Builder. This gives you the flexibility to create any kind of custom residue. The added atoms inherit the residue name and number and the chain name from the parent residue, so any extra groups you add are considered part of the residue. If you are creating a custom residue, you might want to rename the residue, which you can do in the Change Atom Properties Panel.

The Residue and Loop Mutation Panel can also be used to perform single-residue mutations to both standard and nonstandard residues, including custom residues. It also allows residue deletion, insertion, and swapping of loops.

For automatic residue mutation with particular goals in mind, the following tools are available. These tools run jobs to perform the mutations and can produce multiple, mutated structures.