TOPO2 uses a sequence along with input provided by the user to create an image of a transmembrane protein. TOPO2 is a simple graphics program and does not even attempt to predict the location of the transmembrane segments it displays.

DESCRIPTION
TOPO2 takes the information provided and creates an image of a transmembrane protein. It finds glycosylation sites and cysteines on the exterior side of the membrane, if requested to do so. It can also color code membrane bound amino acids with the following characteristics: acidic and basic amino acids, amine groups, those containing hydroxyl groups, prolines and aromatic amino acids. Any other amino acid of interest throughout the protein can also be color coded if its position is known. Consecutive sequence regions or signature regions can also be colored.

TOPO2 is the latest version of an earlier program called TOPO. The earlier software was written from a hard copy perspective and was governed by the restrictions placed on it by graphics drivers of the time. TOPO2 has been completely rewritten in Python to eliminate the problems with the older program.

To better understand the operation of the TOPO2 program, a description is given of what is meant by the various items to be filled in on the web page.

As with all such programs, a sequence is needed to work with. In the case of TOPO2, the sequence needs to be that of a protein for which you have some sort of transmembrane segment information. See the information given here for format details. Information needs to entered in sequential order starting at the N terminus end of the protein and proceeding to the C terminus. Sequence data is modified in the order of the highlighting features, so it is possible for a residue to change its coloration based on later steps in the highlighting process.

Number of segments

Enter the number of transmembrane segments found in the protein.

Desired segment information

In the box, enter the starting position, ending position and type of each segment. TOPO2 can handle two types of transmembrane segments. Type 1 completely crosses the membrane. Type 2 only enters the membrane region and exits again from the same entry side. Segment information is entered by typing the data into the box using either a space or tab to separate each item. Enter the information for each segment on a separate line.

In the following example line, 20 is the start position, 40 the ending position, and 1 is the segment type.

20 40 1

Protein start

Click the radio button which reflects the starting point of the protein with respect to the membrane. Outside usually means on the "Extracellular" side of the membrane and inside the "cytoplasm" side. In cases were these terms don't match the protein's environment, the intermediate xml file can be edited to contain the proper names. This option is only available to those running TOPO2 software on their own machine.

Outside residues

TOPO2 is capable of highlighting residues of interest throughout the protein. It contains code to allow for the selection and hightlighting of residues that are on the outside or "extracellular" side of the membrane. To work with these residues, check the special outside residues box.
cysteine residues

To color code all the outside cysteine residues, check the Show cysteine residues box and then from the pull down menus select the desired shape and color values.

N-glycosylation sites

To have the program check for N-glycosylation sites in the outside portion of the protein, check the Show N-glycosylation sites box and them from the pull down menus, select the desired shape and color to use.

Membrane residues

The program is capable of highlighting 6 different types of residues located within the membrane layer. To highlight all these residue types with the membrane, check the Show membrane residues box.
Charged residues

TOPO2 will highlight all charged residues within the membrane layer, if so directed. To do this, check the Show charged residues box and then select from the pull down menus the appropiate shape and color to use for the acidic and basic residues.

Amine residues

All the amine residues inside the membrane can likewise be highlighted by checking the Show amine residues box and selecting the desired shape and color to use.

OH residues

Highlight all residues containing hydroxyl groups within the membrane by checking the Show OH residues box and selecting the desired shape and color to use.

Aromatic residues

All aromatic residues within the membrane layer can be highlighted by checking the Show aromatic residues box and selecting the shape and color to be used.

Prolines

To hightlight all prolines within the membrane, check the Show proline residues box and pick the appropiate shape and color.

TOPO2 can also highlight any other residues with the protein that don't fall into any of the previous categories. There are two different means of doing this. One highlights regions of consecutive residues, the other individual residues. To do this, the available shapes and colors need to be used. These are given below.

Available shapes (code shape)                    Available colors
0 none        1 circle                  white     black      red      orange
2 square      3 hexagon                 blue      cyan       green    yellow
4 up arrow    5 down arrow              magenta   purple     brown    dgreen
6 diamond     7 star                    gray      grey       lgray    lgrey

Signature regions

Regions of consecutive residues to be highlighted are known as signature regions. To enter this data, check the Show signature regions box and then enter the number of such areas. This number must match the number of information lines entered in the associated text box. Information in the text box relates to the starting position of the region, its ending position, the shape to be used and the color. These items should be separated from one another by either a space or a tab.

In the following example line, 20 is the starting position, 30 the ending position, 3 is the code for the desired shape (a hexagon) and orange the color to use for this region.

20 30 3 orange

Special residues

Individual residues to be highlighted are known as special residues. These residues can be anywhere in the protein. Since this is the last highlighting task done by the program, such residues can also occur within signature regions.To enter this data, check the Show special residues box and then enter the number of such residues. This number mustmatch the number of information lines entered in the associated text box. Information in the text box relates to the location of the residue, and the shape and the color to be used. These items should be separated from one another by either a space or a tab.

In the following example line, 77 is the residue's location, 5 is the code for the desired shape (a down arrow) and purple the color to use.

77 5 purple

Show residue characters

For publication purposes, it might be desired not to display the residue characters in the image. By checking the no button an image will result without residue single letter codes being given.