Classification of Protein Structures

Topology diagrams are useful for classification of protein structures... 

Classification of Protein Structures Based on Convex Hull Representation by Integrated Neural Network. 

Figure 1.15 Classification of protein structure according to Levitt and Chothia.15 The protein is viewed from such an angle that most segments of secondary structure are seen end on. Each strand of a j8 sheet is represented by a square. The front end of each a helix is represented by a circle. The segments that are close in space are close together in the diagram. The segments are connected by bold or thin arrows (from the N- to the C-terminus) to indicate whether the connection is at the near or the far end. The approximate scale is diameter of a helix = 5 A j8 strand = 5 X 4 A separation of helixes = 10 A separation of hydrogen-bonded j8 strand = 5 A separation of nonhydrogen-bonded strands = 10 A.

Nucleic acids have a primary, secondary, and tertiary structure analogous to the classification of protein structure. The sequence of bases in the nucleic acid chain gives the primary structure of DNA or RNA. The sequence of bases is read in a 5 -> 3 direction, so that you would read the structure in the next figure as ACGT. See Figure 8-1. 

Biochemically there are four major classifications of protein structure primary (amino acid sequence), secondary (local spatial arrangement), tertiary (overall 3D structure) and quaternary (protein complex stmcture). (Figure 1.8)... 

The elucidation of so many structures has allowed a successful classification of protein structures [7,8] it has laid the basis for certain predictive methods [9,10], and it has given insight into the possible evolutionary origins of proteins [11-13]. Our understanding of biological function in terms of structure has not increased so fast. This has turned out to be a more difficult problem. In the case of enzymes, a description of several different states of the protein complexed with substrate, intermediates and products together with necessary co-factors and activators is required. Often these different states can only be achieved by co-crystallisation, and even then it may be difficult to trap the necessary conformation. To date, it is... 

Key words Structural biology, Database mining, Classification of protein structures, Pharmacophore, Hit finding, Binding site mapping, GRID/CPCA... 

Structural Classification of Proteins (SCOP), Cambridge, UK Major structural classification of protein structures and domains (Murzin et al.) http // scop.mrc-lmb.cam.ac.uk/ scop/ Cambridge University, UK, A. Murzin et al. [245, 284]... 

M. Levitt and C. Chothia (81) constructed taxonomic classifications of protein structure and noted that a helix and (3 sheet structures within protein domains are organized in a limited number of ways. The four main subcategories are named a for a-helical proteins, 3 for proteins that are primarily composed of 3 sheets, a + 3 for proteins with both a helices and 3 sheets, and a/3 for those proteins that have alternating a-helix- and 3-sheet arrangements. 

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