The Protein Editor provides tools to modify the sequence of a protein by mutating, inserting, or deleting residues. There are also tools to enter a new sequence, generate an MSF from a sequence, or change the hydrogen representation of the molecule.
The Protein Design Edit Protein utility has tools for mutating, inserting, and deleting residues. The same functions can be applied to MSFs or sequences.
The definitions of the composition and structure of amino acids as used in mutation, insertion, and regularization is taken from the structure definition file $HYD_LIB/protein_structure.gsd. It is possible for users to add new residue definitions to the file or change existing ones - see Appendix D..
After a structure has been modified, the conformation initially generated may be energetically unfavorable. For example, inserting an extra residue into a good structure is certain to be energetically unfavorable. In order to accommodate the change, neighboring residues to the one edited may need to be moved. A regularization tool is provided which will attempt to find an energetically reasonable conformation, but note that it usually starts from a very poor conformation and can only find the local minima. For changes which involve inserting and deleting residues the tools in the Model Backbone utility probably need to be used.
Mutated residues are given geometrically sensible structures and, as far as possible, the side chain torsions are copied from the old side chain. A local conformation optima will be found if the Regularization tool is active.
Inserted residues are generated in a linear conformation appended to the residue before or after the insertion. Each new residue is given a default ID based on the preceding existing residue. For example, a residue inserted after residue 10 will get an ID of 10.1. If several amino acids are inserted, the fractional number is incremented by one for each: 10.2, 10.3, and so on.
Deleted residues are simply removed from the structure. No other changes are made automatically. The sequence can be renumbered by the Renumber Residues tool.
After inserting new residues it is advisable to model the side chains. The Auto Model tool on the Model Side Chains palette will do this (see Chapter 9) and, to simplify the procedure, the Protein Editor utility automatically writes a selection file, edit_side_sel.rsd which lists the inserted residues.
Segments can be created or merged using the Atom Property Editor on the Edit pulldown. The residue table in this utility has a column containing the segment name. If a segment name is changed then the edited residue, and all residues before it in the same segment, will be assigned to a new segment with the new name. To merge two segments, double click the segment column header to bring up a dialog box which has tools for merging segments.
Hydrogen atoms are added to those atoms with atom types which indicate that they are extended atoms. Extended atoms types are used to denote atoms which should have hydrogen atoms attached. For hydrogen addition to work correctly the atoms must be correctly typed. The Apply Dictionary utility on the Edit pull-down retypes atoms if necessary.
Hydrogen atom coordinates are taken from templates in the file $HYD_LIB/hydtpl.dat. There are templates for all the extended atom types commonly found in proteins. To derive the hydrogen coordinates, the guide atoms in the template are superposed over the extended atom and two neighbors in the protein and the hydrogen coordinates copied from the template hydrogen atom coordinates. The atom type of the extended atom is changed to the appropriator non-extended form.
The Protein Editor interface consists of a conventional palette of editing tools and an amino acid selection palette.
This palette consists of a list of the standard amino acid types (non-standard types are listed in a scrolling list accessed via the Non-standard tool). As you enter a sequence of amino acids, they are displayed in the Sequence Viewer colored red.
Presents a scrolling list of all amino acids in the protein structure definition file which are not one of the twenty standard amino acids.
This tool displays a dialog box to enter the sequence as a string of one letter amino acid codes from the keyboard.
This tool removes the last amino acid entered. The tool can be used repeatedly.
This tool exits from the palette without saving any sequence entered, so no insert or mutate action is applied.
This tool exits from the palette and applies the insert or mutate action.
If this tool is active, then after each mutate, insert or delete function the structure will be regularized. The regularization tool is described more fully in chapter 8. By default, only the changed residue is regularized after mutation but after insertion or deletion two residues on either side of those changed will also be regularized. The number of residues regularized can be changed by the Regularization Options tool.
The regularization method and options are described in the Model Backbone chapter.
When one of these tools is selected then all active structures will be converted to the designated hydrogen representation.
These tools insert residues before or after a residue. Once picked, these tools remain active and highlighted until they are toggled off or another editing tool is toggled on. After choosing this option, you pick a residue on the molecule or Sequence Viewer, and then choose one or more residues to insert before or after the specified residue.
While this tool is active you to can pick a residue on the molecule or Sequence Viewer and then select a new residue type from the amino acid selection palette. Once picked, this tool remains active and highlighted until it is toggled off or another editing tool is toggled on.
This tool mutates a specified range of the sequence. The Pick Range palette enables you to select the range of residues to mutate. The Amino Acid Selection palette is displayed and the changed residues are shown in red in the Sequence Viewer.
While this tool is on you may pick a residue on the molecule or Sequence Viewer and it will be deleted. Once picked, this tool remains active and highlighted until it is toggled off or another editing tool is toggled on.
This tool activates the Pick Range palette from which a range of residues can be selected for deletion.
Select one terminal residue on either the molecule or the Sequence Viewer and a palette like the amino acid selection palette (but with the appropriate terminal groups) will be displayed, allowing you to select a new group. It is not appropriate to change the terminal of a sequence.
You should select a cystine residue by picking from either the Sequence Viewer or by picking one atom in the residue on the molecule. If that cystine is already part of a disulfide bond, then that bond will be broken. If it is not disulfide bonded, then it will make a bond to any neighboring cystine residue. It is not appropriate to make or break disulfides in sequence only data.
All residues in a range are numbered consecutively from the first residue ID. This tool activates the Pick Range palette to pick a range of residues. You are then prompted for the ID of the first residue in the range, which, by default, is the current ID. If an insertion code is entered, all residues in the range are given the same ID as the first residue and they are given incremental insertion codes which follow from the entered insertion code.
The amino acid selection palette is presented and you can enter a sequence which will be displayed in the Sequence Viewer below any existing sequences. On exiting the amino acid selection palette you are prompted for a name for the new sequence.
By default, MSFs will be created for all currently active sequences and by default the new file is given the same name as the sequence. The sequence is removed from the selection and replaced by the MSF.
This tool exits from the palette. If any structures have been edited but not saved to MSF you will be prompted to save them. If they are not saved then the structures will revert to those currently saved in the MSF.