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The Protein Chart

2010; Wiley; Volume: 38; Issue: 2 Linguagem: Inglês

10.1002/bmb.20342

1539-3429

Eric Martz,

Genetics, Bioinformatics, and Biomedical Research

Richard C. Garratt and Christine A. Orengo, Wiley-VCH, 2008, ISBN: 978-3-527-31963-3, $19.99 or €14.90. A six-page plastic-laminated reference chart in color on lightweight A4 cardstock (threefold-out double-sided panels, 11 × 8.3 inches/28 × 21 cm). Eric Martz*, * Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003. Suitable for college biochemistry students as well as biochemical educators and researchers, The Protein Chart packs an astonishing amount of information about protein 3D tertiary and quaternary structure into a well-organized, compact six-page reference chart. The title is misleading: The Protein Chart covers only a relatively narrow aspect of protein science. Derived from the CATH protein structure classification, the Chart fills five pages, with an attractively designed cover occupying the sixth. “CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class (C), Architecture (A), Topology (T), and Homologous superfamily (H)” (www.cathdb.info). The bulk of the chart, three pages, is devoted to tertiary domain structure. There are 26 domain architectures (columns), each illustrated with 1–5 structures representing fold groups (rows). Each example shows a ribbon schematic, colored by secondary structure. The domain architectures are divided into four classes: alpha proteins (17 examples), beta proteins (28 examples), alpha/beta proteins (32 examples), and knots and fibers (nine examples). These three pages thus contain 86 examples of fold groups in a hierarchical tabular format. Each example includes the fold name, the PDB (Protein Data Bank) identification code, chain identifier within the PDB entry and domain number, the CATH code for fold group, a “secondary structure string”, an average length in residues with standard deviation, and an indication of whether the domain occurs in eukarya, archaea, or bacteria. The functions of the molecules containing the members of each fold group are also indicated, using eight categories of functions. A full page is devoted to quaternary structure (oligomers), divided into columns according to rotational symmetry – the number of identical subunits per 360 degree turn. Four to five examples are in each column, annotated with the name of the protein, the PDB identifier, the number of subunits, and the point group symmetry (in both Schoenflies and international nomenclature), and the presence or absence of dihedral symmetry. The contributions of oligomerization to structure or function are also indicated, using eight categories. A half page is devoted to 10 examples of basic topologies of secondary structure (Greek key, jelly roll, immunoglobulin domain, Rossman fold, etc.), and a half page to important structural motifs (helix-turn-helix, EF-hand, leucine zipper, zinc finger, etc.). There are some minor inadequacies, which perhaps could be addressed in a second edition. A few things were unclear, and I wished that some of the blank areas (nearly one-quarter of the three pages on domains is blank) had been used to explain and clarify. Alternatively, a website with explanatory notes would be very welcome. (No website was mentioned except cathdb.info, where I found no mention of The Protein Chart.) From the following statement, I could not tell what the tabulated percentages represent: “The population given as a percentage for each architecture is calculated from the 527 genomes present in Gene3D version 6.0.” The function “binding” seemed to deserve some clarification, as did “domain number”. Is the “number of subunits” (on the oligomer page) synonymous with “number of protein chains”? It would have been interesting to know how many of the 37 oligomer examples were homo-oligomers (most, it appeared to me, with one hetero-oligomer example being the proteasome 1pma). Also, as average lengths were given for each of the 86-fold group examples, it would have been interesting to know the total number of structures in each fold group. The uninitiated could be left with the impression that this chart gives an overview of all that is known about protein 3D structure. A more complete impression could have been achieved had the widespread occurrence of intrinsically unstructured protein been mentioned, illustrated with a few examples of sequences that adopt stable uniform structures only when folding against a previously folded domain. The Protein Chart offers an overview and sampling of the breadth of protein 3D tertiary and quaternary structural knowledge and classification that is eminently useful and at the same time quite beautiful. The convenient inclusion of PDB accession codes makes it easy to further explore any of the 123 examples. There is plenty to absorb and to ponder both for beginners and for structural biologists. It is difficult to imagine any better way to convey the state of the art so graphically and succinctly.