Building protein diagrams on the web with the residue-based diagram editor RbDe

Abstract

The residue-based diagram editor (RbDe) is web-based software that greatly simplifies the construction of schematic diagrams of proteins. Residue-based diagrams display the sequence of a given protein in the context of its secondary and tertiary structure. Such diagrams are frequently used to summarize mutations or sequence features, in the context of the overall topology of a protein. The initial version of RbDe was designed for transmembrane proteins and has enabled many users to create diagrams of large systems such as G protein-coupled receptors or transporters. We present an extended diagram editor that supports other families of proteins. Users can now import custom-diagram layouts, use them to render members of any protein family and generate high-quality output for publication purposes. RbDe is available free over the web, at http://icb.mssm.edu/crt/RbDe

Figure 1

Diagram of the human dopamine transporter. The diagram was produced through the web with the first release of RbDe. Residues are colored according to residue types (the color scheme colors residues of similar physicochemical properties in a similar way) and the diagram indicates the element of secondary structure (transmembrane helices) and the connecting loops. The white circles represent contiguous stretches of residues which are omitted from this diagram.

Figure 2

Progression of a typical user through the web application for a typical use of RbDe. Information is collected as the user progresses through the sections of the web software (seq: sequence; ss: secondary structure; layout: layout of the diagram on the page, see text for details; colors: colors of specific residues or color scheme to color the entire diagram by residue type; URLs: hyperlinks from residues to documents on the web). The diagram is built and refined iteratively as the user proceeds through the application.

Figure 3

(A) Fragment of a layout input file. A layout is defined by a list of subunits. Each subunit has a type, which determines how the residues in the subunit will be rendered. Some subunit types (e.g. helices and strands) are given a direction. The direction is a vector that controls the global direction along which residues of the subunit will be rendered. Other subunits, such as subunits to represent loops that connect the first type of subunits, are given a spacer. The spacer is a vector that defines how much the first residue of the subunit is separated from the last. Units of direction and spacer are pixels in the coordinate system shown on the right. (B) Fragment of a diagram built with the layout parameters shown on the left. Yellow arrows represent the direction of helices and strands. Green arrows represent the spacers of the loops.

Figure 4

The calmodulin protein sequence is rendered and shown with two diagram layouts based on the crystal structure of the molecule (A) and the calmodulin-trifluoperazine complex (B). The diagrams reveal the structural rearrangement upon ligand binding.