Protein topology, representation structure

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 ... 

Visnalization is an efficient way to utilize the human ability to process large amounts of data. Traditional visnalization methods are based on clustering and tree representation, and are complemented by projecting objects onto a Euclidean space to reflect their structural or functional differences. The data are visualized without preclustering and can be explored dynamically and interactively, e.g., in protein topology and gene expression. 

Figure 89 illustrates two different tries at simplified representation of the globin structure. For reference, Fig. 89a shows the hemoglobin /3 chain in stereo. Figure 89b shows the globin structure schematically as two layers of helices with the elements in one layer approximately perpendicular to those in the other layer this can be contrasted with a possible description of the up-and-down helix bundles as two layers with their elements approximately parallel to each other. The perpendicular layers provide a rather successful simple schema for the globin structure, but unfortunately there are no other proteins that can be adequately described as two perpendicular layers of helices. Also, specification of the topology in this scheme is cumbersome, since the chain skips back and forth between layers. 

Koch et al. [111] have discussed the use of graph theoretical techniques in an attempt to find rules to relate beta sheet topology to amino acid sequence and for the comparison of beta sheet structures. They defined a graph representation for every protein in the PDB that contains beta sheets, notations and graphic representations for sheets which described the sequential and topological neighbourhoods of the strands, and constructed tools for substructure searches of this database. 

The ribbon model in Figure 5.5d shows the organization of the structural path of the secondary structure elements of the protein chain (a-helix and j8-sheet regions). This representation is very often used, with the arrowheads indicating the N-to-C-terminal direction of the secondary structure elements, and is most effective for identifying secondary structures within complex topologies. 

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... 

One can describe a molecule in many ways and the same applies to bioisosteres. Molecular descriptor methods are covered in the third part by the application of different representations. A number of computational approaches to bioisosteric replacement are covered in chapters on physicochemical properties, molecular topology, molecular shape, and the use of protein structure information. Each chapter covers many common methods and overviews of when best to apply these methods, and where they have been successfully applied. 

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. ...

Highly simplified models of protein structure embedded into low coordination lattices have been used for tertiary structure prediction for almost 20 years [65, 66, 75]. For example, Covell and Jemigan [64] enumerated all possible conformations of five small proteins restricted to fee and bcc lattices. They found that the nativelike conformation always has an energy within 2% of the lowest energy. Virtually simultaneously. Hinds and Levitt [28] used a diamond lattice model where a single lattice unit represents several residues. While such a representation cannot reproduce the geometric details of helices or P-sheets, the topology of native folds could be recovered with moderate accuracy. 

Fig. 2.17. Schematic representation of topological connectivities of p pleated sheets found in proteins of known three-dimensional structures (courtesy of Richardson, 1977). From top to bottom, the examples are presented according to the increasing number of p strands forming the sheet (from left to right according to the percentage of antiparallel connections). Arrows indicate the strands of P sheet in the plane of the paper. Cross-over connections which are...

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