Taxonomy, of proteins

On the basis of simple considerations of connected motifs, Michael Leviff and Cyrus Chothia of the MRC Laboratory of Molecular Biology derived a taxonomy of protein structures and have classified domain structures into three main groups a domains, p domains, and a/p domains. In ct structures the core is built up exclusively from a helices (see Figure 2.9) in p structures the core comprises antiparallel p sheets and are usually two P sheets packed... 

Richardson, J.S. The anatomy and taxonomy of protein stmcture. Adv. Prot. Chem. 34 167-339, 1981. Rossmann, M.G., Argos, P. Protein folding. Annu. Rev. 

Figure 5-1. Ramachandran plot of the main chain phi (< ) and psi (T) angles for approximately 1000 nonglycine residues in eight proteins whose structures were solved at high resolution. The dots represent allowable combinations and the spaces prohibited combinations of phi and psi angles. (Reproduced, with permission, from Richardson JS The anatomy and taxonomy of protein structures. Adv Protein Chem 1981 34 167.)...

The vast accumulation of information about protein structures provides a fresh opportunity to do descriptive natural history, as though we had been presented with the tropical jungles of a totally new planet. It is in the spirit of this new natural history that we will attempt to investigate the anatomy and taxonomy of protein structures. 

FIGURE 2.2 The alpha (a) helix, showing the pattern of intrachain hydrogen bonds that stabilize the structure, and the radial extension of amino acid side chains from the helix axis. (Adapted from Richardson, J.S. [1981]. The anatomy and taxonomy of protein structure. Advances in Protein Chemistry, 34, 167—339, copyright 1981, with permission from Elsevier Science.)... 

S Hcnikoff, EA Greene, S Pietrokovski, P Bork, TK Attwood, L Hood. Gene families the taxonomy of protein paralogs and chimeras. Science 278 609-614, 1997. 

Figure 4.9 Two major types of ft (tight) turns. In type II, R3 is usually glycine. (Reproduced with permission from Richardson JS. The anatomy and taxonomy of protein structure. Adv Prot Chem 34 167-339, 1981.)...

Figure 4.13 Anatomy of selected proteins. (A) The /3 subunit of hemoglobin carrying a heme molecule (B) triose isomerase and (C) /3-lactoglobulin carrying a molecule of vitamin A. Spirals represent helix segments, and the broad arrows are pleated sheet polypeptide segments showing the direction from the N to the C terminus. (A and B reproduced with permission from Richardson JS. The anatomy and taxonomy of protein structure. Adv Prot Chem 34 168-339, 1981. C reproduced with permission from Papiz MZ, Sawyer L, Eliopoulos EE, North ACT, Findlay JBC, Sivaprasadarao R, Jones TA, Newcomer ME, Kraulis PJ. The structure of beta-lactoglobulin and its similarity to plasma retinol-binding protein. Nature 324 383-385, 1986.)...

Richardson JS (1981) The anatomy and taxonomy of protein structure. Adv Protein Chem 34 167-339... 

Richardson, J. S. (1981) The Anatomoy and Taxonomy of Protein Structure, Adv. Protein Chem. 34, 167-339. 

Proteins Structures and Molecular Properties, 2nd ed., Thomas E. Creighton, 1993, Freeman and Co., New York. "The Anatomy and Taxonomy of Protein Structure," J. S. Richardson, 1981, Adv. Prot. Chem., 34 167339. 

Fig. 7.8. Ribbon drawing showing the arrangement of secondary structures into a three-dimensional pattern in domain 1 of lactate dehydrogenase. The individual polyjjeptide strands in the six-stranded P-sheet are shown with arrows. Different strands are connected by helices and by nonrepetitive structures (mrns, coils and loops), shown in blue. This domain is the nucleotide binding fold. NAD is bound to a site created by the helices (upper left of figure.) (Modified from Richardson JS. Adv Protein Chem. The anatomy and taxonomy of protein structure 1981 34 167).

Fig. 7.17. Structure of the Vl and Cl domains of IgG. Layers of antiparallel 3-sheets are stacked in these domains, which have been referred to as collapsed -barrels. The antigen binds between the Vh and Vl immunoglobulin folds, and NOT in the barrel. The Cl domain is also called the immunoglobulin fold. (Top modified from Richardson JS. Adv Protein Chem. The anatomy and taxonomy of protein structure 1981 34 167 bottom reprinted in part with permission from Edmundson AB, et al. Biochemistry 1975 14 3954. 1975 American Chemical Society.)...

Rossmann and Argos (1977) defined structural equivalence indicating that any residue or structural elements (a helix, p pleated sheet) is coincident with that of another molecule by superposition. It is called positive equivalence when similarly directed and negative equivalence when oppositely directed. Topological equivalence refers to a run of positive equivalence. According to these methods, a taxonomy of protein three-dimensional structure was developed. 

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