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.
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.
In the following example line, 20 is the start position, 40 the ending position, and 1 is the segment type.
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
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
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
The original TOPO program was created from a graphics perspective. It is based on the limitations imposed by postscript drivers on the physical page. When the size of a starting, ending or loop portion of the sequence exceeds the limits for a single page image, additional pages are created which will then have to be manually cut and pasted onto the main page to produce a final image for publication.
TOPO2 is free from these restrictions. It produces a single output file containing all the data in a single image. This information is in the form of an XML file which is processed by additional software to get the final image file. That image is either contained in a postscript file or a PNG file.
TOPO2 creates transmembrane segments in a variety of lengths. It can handle partial (6 - 79 residues) as well as completely crossing transmembrane (6 - 42 residues) segments. The small segment sizes are to allow for the display of transmembrane segments produced by beta-sheets. The program crashes when too small or too large of a transmembrane segment is used.
Suggestions for the original TOPO program were from students in Dr. Kevin Bertrand's Lab (Biochemistry/Biophysics Department at Washington State University). Further interest was shown by Dr. Robert Speth of VCAPP at WSU and later by students and faculty at the University of California, San Francisco. Software development support was received from the VADMS Center (WSU), a 1996 grant to Dr. Speth from the Adler Fund, College of Veterinary Medicine (WSU), and the Sequence Analysis & Consulting Service of the UCSF Computer Graphics Laboratory.
This program was written by Susan Jean Johns, of SACS at UCSF (E-mail: johns at cgl.ucsf.edu), formerly of the VADMS Center, Biochemistry/Biophysics Department at WSU. Transmembrane expertise supplied by Dr. Robert Speth of WSU for the TOPO program.