Protein structural representations

The two search algorithms that process the protein-structure representation described in the previous paragraph derive from work carried out previously in... 

Figure 4 Structure and reaction mechanism of ALAS, (a) Crystai structure of Rhodobacter capsulatus ALAS. Each subunit of the dimeric protein consists of an N-terminai domain (red), the centrai cataiytic domain (biue), and a C-terminai domain (green). Each monomer contains a covaientiy attached PLP (shown in sticks representation). This and aii other protein structure representations were generated using PyMOL (http //pymoi.sourceforge.net/). (b) The ALAS reaction proceeds via formation of a quinonoid intermediate, reiease of CoA and CO2, and formation of a second quinonoid intermediate before ALA is reieased from the enzyme.

S. Sun, Reduced representation model of protein structure prediction statistical potential and genetic algorithms. Protein Sci. 2 (1993), 762-785. 

All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves. These are difficult to illustrate. Therefore we use different types of simplified representations, including space-filling models ball-and-stick models, where atoms are spheres and bonds are sticks and models that illustrate surface properties. The most detailed representation is the ball-and-stick model. However, a model of a protein structure where all atoms are displayed is confusing because of the sheer amount of information present (Figure 2.9a). 

Fig. 2. Protein backbone representations of (a) the 2[4Fe-4S] ferredoxin from Peptococcus aerogenes, (b) the proposed structure of the FA/FB-binding protein of PSl based on the 4 A crystsd structure (25), and (c) the [3Fe-4S][4Fe-4S] ferredoxin from Sulfolo-bus acidocaldarius. Ligands to clusters Fa and Fb, important residues as well as the loop extension (see text) EU e highlighted in darker gray.

Figure 4.14 Diagrammatic representation of (a) oxy-radical>mediated S-thioiation and (b) thiol/disulphide-initiated S-thiolation of protein suiphydryl groups. Under both circumstances mixed disuiphides are formed between glutathione and protein thiois iocated on the ion-translocator protein resulting in an alteration of protein structure and function. Both of these mechanisms are completely reversible by the addition of a suitabie reducing agent, such as reduced glutathione, returning the protein to its native form.

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

Another useful type of representation for protein structures is the diagonal plot. It is a matrix with the amino acid sequence number along both axes, in which either distance between the respective a-carbons or contact between the respective residues is plotted for each possible pair of residues (see Fig. 10). The diagonal plot is probably the most successful method yet devised of quantitatively mapping the... 

Figure 10 N M R structural analysis of carrier domains. Three conformations of the PCP domain from tyrocidine synthetase (brown box) and the NMR structure of the related AGP domain from a polyketide synthase. The star symbol signifies the position of the conserved phosphopantetheinylated serine residue. The protein ribbon representations are rainbow colored from red (N-terminus) to violet. PDB codes A/H state, 2GDW H-state, 2GDX A-state, 2GDY AGP, 2AF8.

State, R. H. and Karplus, M. (1995) Zinc binding in proteins and solution a simple but accurate nonbonded representation. PROTEINS Structure, Function, and Genetics 23, 12-31. 

An outstanding summary of protein structural patterns and principles the author originated the very useful ribbon representations of protein structure. 

In this figure, and in figures throughout the book, we represent transmembrane protein segments in their most likely conformations as a helices of six to seven turns. Sometimes these helices are shown simply as cylinders. As relatively few membrane protein structures have been deduced by x-ray crystallography, our representation of the extramembrane domains is arbitrary and not necessarily to scale. 

Figure 16.3 A schematic of the myosin protein, (a) Representation of the different structural regions in the myosin and (b) a representation of the localities where the various activities of the enzyme are found. From Biochemistry, 4th Edition, by Stryer, p. 395. 1995, 1988, 1981, and 1975, by Lubert Stryer. Used with permission by W. H. Freeman and Company.

For several years we have been involved in a wide-ranging project to develop methods for the representation and searching of the three-dimensional (3-D) protein structures in the Brookhaven Protein Data Bank [28, 29], Our work derives from the graph-theoretic methods that are used for the storage and retrieval of information pertaining to both two-dimensional (2-D) and 3-D small molecules [1, 58]. 

Above we have described the use of graph theoretical algorithms to identify all occurrences of a user-defined pattern of residues in a database of protein structures. The residues in a protein or a query pattern are represented in a highly simplified form that consists of two pseudo-atoms and the relative orientations of pairs of sidechains are defined by the distances between pairs of these pseudo-atoms. Despite the simplicity of the representation, our tests with a variety of patterns demonstrate the usefulness of the methodology. 

Fig. 11.12 Structural representation of protein modified with polymers. The polymer dictates the hydrodynamic volume, the stability to proteolysis, and antigenicity of the conjugate.

Sequence analysis is a core area of bioinformatics research. There are four basic levels of biological structure (Table 1), termed primary, secondary, tertiary, and quaternary structure. Primary structure refers to the representation of a linear, hetero-polymeric macromolecule as a string of monomeric units. For example, the primary structure of DNA is represented as a string of nucleotides (G, C, A, T). Secondary structure refers to the local three-dimensional shape in subsections of macromolecules. For example, the alpha- and beta-sheets in protein structures are examples of secondary structure. Tertiary structure refers to the overall three-dimensional shape of a macromolecule, as in the crystal structure of an entire protein. Finally, quaternary structure represents macromolecule interactions, such as the way different peptide chains dimerize into a single functional protein. 

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 ... 

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