Building Biopolymers

peptides, proteins, DNA, RNA

To make it easy to build biopolymers—peptides (both standard and nonstandard), DNA, and RNA—Maestro recognizes when you are adding an amino acid or a nucleic acid to a chain, and adds the incoming residue at the right location for building a biopolymer. If you have a single amino acid in the Workspace, the new amino acid is added at the C-terminal end; otherwise it is added at the free end (based on the selection). For a nucleic acid chain the build direction is 5'→3'. For double-stranded DNA you can build onto one or both chains: select an atom in both 3' termini to add a new nucleic acid to both chains at once. Any capping group is replaced by the incoming amino or nucleic acid. When picking a residue to add another amino or nucleic acid to, you can pick any atom in the residue: it does not have to be the atom to which the incoming acid will be attached.

To help in creating a chain, the Fragments Panel has an option for shifting the selection to the last added unit, Move selection for chaining. This option is displayed when you choose any of the amino acid or nucleic acid items from the Fragments option menu. With this option, you can start with the chain end selected, then click on the acids you want to add, and they are added to the end of the chain. Without this option, you would have to pick the last added acid in the Workspace each time so you could continue to build the chain.

When you select Move selection for chaining, you can also make settings for the joining geometry and secondary structure of the chain. Click Options, and choose the desired settings from the options menu. You can set custom phi and psi angles if the available secondary structure elements do not suit your needs. When you choose Custom Angles, a dialog box opens for each fragment added, so you can set the phi and psi angles; if you cancel in this dialog box, the amino acid is not added.

If you are building onto an amino or nucleic acid with a fragment of some other type, the normal building behavior applies: the fragment is added to the selected atoms, and inherits the residue properties (such as name and number) of the amino or nucleic acid it is attached to.

You can also build peptides, DNA, or RNA from a sequence, using the Build Biopolymer from Sequence Dialog Box. In this dialog box you can specify the secondary structure to use for a peptide, either by choosing a standard or specifying a custom secondary structure or set of angles. For DNA you can choose the helix conformation and build either single-stranded or double-stranded DNA.