Protein topology cartoons

Protein topology cartoons (TOPS) are two-dimensional schematic representations of protein structures as a sequence of secondary structure elements in space and direction (Flores et al, 1994 Sternberg and Thornton, 1977). The TOPS of trypsin domains as exemplified in Figure 4.9 have the following symbolisms ... 

Figure 12.1. Protein topology cartoons of representative protein domains. The 2D schematic drawings of some representative domains are illustrated in TOPS cartoons (originally retrieved from TOPS server) in which the domain start at N and ends at Ci+1. a- (and 310) Helices and / strands are represented by circles and triangles, respectively, according to the symbolisms described in Chapter 4.

STO TCP TOPS TrEMBT tRNA UPGMA URT UTR UV WWW (www) Slater-type orbital transmission control protocol protein topology cartoons translated EMBT transfer (soluble) ribonucleic acid(s) unweighted pair group method using arithmetic means uniform resource locator untranslated region ultraviolet World Wide Web... 

To search for TOPS cartoons at http //tops.ebi.ac.uk/tops/, select Browse the Atlas of topology cartoons and Browse HTML page version to open the query form (Figure 4.13). Enter PDB ID on the Protein code query box (Chain query box can be left blank). The search may request a choice of the chain (if more than one chains are available) and returns TOPS atlas information listing the protein of your choice and representative protein in atlas. Click to view the TOPS cartoon(s) of the representative protein. Right click on the diagram to save the TOPS cartoon as cartoon.gif. 

Thus, the H,K-ATPase in microsomes is a useful model to develop new methods to determine protein topology. The cartoon in Figure 2 illustrates that the H,K-ATPase is a heterodimer composed of two subunit proteins an a-subunit of 1035 amino acids, traversing the membrane either 8 or 10 times (13), with most of its mass cytoplasmically disposed (and therefore outside the vesicles) and a glycosylated P-subunit of 300 amino acids, traversing the membrane once and, except for a short cytoplasmic tail, with most of its mass on the extracellular side (inside the vesicles). 

TOPS Visualization and Structure Viewers Topology cartoons of secondary structure arrangements of proteins from DSSP input http //www.sander.embl-ebi.ac.uk/tops EBI, Cambridge, UK, D. Gilbert et al. [307]... 

Figure 3 shows a cartoon representation of the topology and secondary structure of the decorin protein core. The overall shape, like that of other LRPs (24), is an arch, or bent solenoid , in which the polypeptide chain follows a right-handed helical path. The inner concave face of the arch is made up of 14 p-strands the first... 

Figure 7 Topology (a) and cartoon representation (b) of the TIM barrel. The protein chain alternates between P and a secondary structure type, giving rise to a barrel P-sheet in the center surrounded by a large ring of a-helix on the outside. This structure, first seen in the triose phosphate isomerase of chicken, has been observed in many unrelated proteins since then. The topology is drawn using TOPS (http //www.tops.leed.ac.uk/), and the cartoon is generated using MOLSCRIPT. ...

TOPS Generates a cartoon of the topology of a protein http //www.tops.leeds.ac.uk/... 

---