Residue and Loop Mutation Panel

In this panel you can create a new structure from an existing protein by residue insertion, deletion, mutation or chirality inversion, or by a loop swap for a string of residues. The new structure can be refined by minimization (with Prime) or simulation (with Desmond).

To open this panel, click the Tasks button and browse to Biologics → Residue and Loop Mutation.

  • Using
  • Features
  • Additional Resources

Using the Residue and Loop Mutation Panel

There are three types of single-point mutation that you can make in this panel: mutation to a standard amino acid, mutation to a nonstandard amino acid, and chirality inversion. The workflow depends on the type of mutation you want to do.

To mutate a single residue to a standard amino acid:

  1. Select Single mutation in the Type section.

  2. Select the residue to be altered either in the Workspace or in the panel's sequence viewer.

  3. Click Workspace Selection in the Original from section.

  4. Choose the amino acid from the option menu in the Mutated to section.

  5. Click Mutate.

To mutate a single residue to a nonstandard amino acid:

  1. Select Single mutation in the Type section.

  2. Select the residue to be altered either in the Workspace or in the panel's sequence viewer.

  3. Click Workspace Selection in the Original from section.

  4. Choose a standard amino acid from the option menu in the Mutated to section.

  5. Select Edit.

    The Workspace structure is replaced by the chosen standard amino acid with the side-chain atoms shown in wire frame representation.

  6. Edit the side-chain atoms to produce the desired nonstandard amino acid.

  7. Deselect Edit.

  8. Provide a three-letter PDB residue name in the dialog box that opens.

  9. Click Mutate.

To invert the chirality of a single residue:

  1. Select Invert chirality in the Type section.

  2. Select the residue to be altered either in the Workspace or in the panel's sequence viewer.

  3. Click Workspace Selection in the Original from section.

  4. Click Mutate.

If you want to refine the mutated structure, click Advanced Refinement Options and make selections in the Refinement Options dialog box:

  • You can choose to run a minimization or a molecular dynamics simulation, or both. The minimization is run first.

  • The minimization can be done in the gas phase or in implicit solvent.

  • You can choose to mimimize the mutated residue only, all residues within a specified distance of the mutated residue, or the whole structure.

  • The simulation can be a regular molecular dynamics simulation at room temperature, or a simulated annealing simulation in which the temperature is raised and then lowered in steps. The latter allows for crossing of barriers. Options for the simulation can be set after the minimization is run.

To insert or delete residues or modify a loop:

  1. Select Deletion, insertion or loop swap in the Type section.

  2. Click Define.

    The Insertions, Deletions, and Loop Swaps Panel opens.

  3. Define the original loop and the insertions, deletions, or replacements in this panel (see the Insertions, Deletions, and Loop Swaps Panel topic for details.)

  4. Choose the number of models to generate and the prediction method, and click Accept.

    The Insertions, Deletions, and Loop Swaps panel closes.

  5. Click Mutate.

No refinement of the loop modification is offered, so you must perform any refinement independently.

If you want to mutate residues to or from cysteine and break or form disulfide bonds, consider using the Cysteine Mutation Panel

Residue and Loop Mutation Panel Features

Type options

Choose the type of residue or loop mutation to perform.

  • Single mutation—Mutate a single selected residue to another residue, standard or nonstandard
  • Invert chirality—Invert the chirality of a single selected residue.
  • Deletion, insertion, or loop swap—Delete or insert one or more residues, or replace a loop with another loop. Click Define to define the changes to be made in the Insertions, Deletions, and Loop Swaps panel.

The tools available in the rest of the panel depend on the option you select.

Sequence viewer

The sequence viewer can be used to import a structure from the Workspace, find residues in the sequence, and select a residue for mutation or inversion. The sequence that is displayed in the sequence viewer is replaced by the sequence of the current Workspace structure when you click Workspace Selection.

The tools in the sequence viewer are:

  • Import button—Import sequences into the sequence viewer from the Workspace.

  • Find Pattern text box—Find a particular pattern in a sequence. You can use an extended PROSITE syntax, which makes use of secondary structure and property information; the syntax is explained in the tooltip. See the Multiple Sequence Viewer/Editor — Toolbar topic for more information.

  • Arrow buttons—These buttons can be used to step through instances of the pattern, in the forward or reverse direction.

  • Sequence display area—This area displays the sequence, its secondary structure assignment (SSA) and annotation of disulfide bonds.

Original from section

Click the Workspace Selection button after the correct residue is selected in the Workspace. The residue can be selected either by picking any of its atoms in the Workspace or by selecting it in the sequence viewer. If the sequence in the sequence viewer is not the sequence of the Workspace structure, it is replaced by the Workspace sequence when you click this button.

To find a particular residue in the Workspace, you can use the Find tool. Type Ctrl+F (⌘F) in the Workspace to display the Find toolbar below the Workspace. You can then choose Residue number or Residue type from the Find menu to choose residues by number or type, then enter the number in the text box or choose the type from the menu, and click the N or P button.

Mutated to section

In this section, you define the mutated residue. This section is only available if you select Single mutation in the Type section. You can mutate to a standard amino acid or a custom amino acid. In both cases, you start by choosing a standard amino acid from the menu.

Amino acid option menu

Choose a standard amino acid from this menu as the mutated residue, or as the basis for a custom amino acid.

Edit option

Select this option to begin editing a standard amino acid in the Workspace to produce a custom amino acid. Deselect this option to exit editing. When you do, a dialog box prompts you to provide a 3-letter PDB name for the custom amino acid. The default is USR. The text on the Amino acid option menu is set to Custom.

To add groups to the structure or to change elements, you can use the 3D Builder panel. Click the Build button to open this panel. With the Add fragments tool, you can select an atom, then click on a fragment to replace that atom with the fragment. You can sketch a structure with the Draw tool, and change the element with the Set Element tool. You might also want to add hydrogens after sketching a structure. You should also use the Minimize tool after sketching the structure and adding hydrogens, to ensure that the structure is not distorted.

Three-letter PDB Name text box

Displays the three-letter code used for the amino acid. You can edit the name in this text box after creating a custom amino acid.

Mutated structure title text box

Provide a new title for the mutated project entry. A default title is constructed from the structure name and mutation details.

Advanced Refinement Options button

Opens a dialog box that offers various refinement options:

  • Choose whether to do a Minimization of the new structure, and if so, whether to do the minimization in the Gas phase or in the presence of an Implicit solvent. Minimization is the fastest option, and is a good choice if the mutated residue is in approximately the right conformation.

    The residues minimized can be limited to just the altered residues, all residues within a given distance of the altered residues, or the entire structure.

  • Choose whether to do a Desmond Simulation with the new structure, and if so, whether to do a Molecular dynamics or Simulated annealing calculation.

    Molecular dynamics is much more time-consuming, but it can sample other parts of conformational space, particularly if you run simulated annealing. Once the structure is mutated and any minimization is done, the protein is prepared for the simulation by adding explicit water molecules. The Molecular Dynamics Panel or the Simulated Annealing Panel opens, and you can make settings and run the simulation, which uses the Desmond molecular dynamics program. For more information on these panels, see Running Desmond Simulations from Maestro.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Residue and Loop Mutation - Job Settings Dialog Box, where you can make settings for running the job.

The job submitted depends on whether a minimization or a simulation was requested in the Advanced Refinement Options dialog box.

Choosing Reset from the Settings button menu resets the panel to its initial state, removes the current sequences from the sequence viewer and loads the sequences for the current Workspace structure into the sequence viewer.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Tutorials

Related Topics