Representation of Protein Structures

Amino acid residues of polypeptide chains are generally represented by the three-letter codes or the one-letter codes. The sequences are written from the left for the N-terminus to the right for the C-terminus, e.g. human lysozyme  

BiontacromoleculeSy by C. Stan Tsai Copyright 2007 John WQey Sons, Inc. 

2 PRIMARY STRUCTURE OF PROTEINS CHEMICAL AND ENZYMATIC SEQUENCE ANALYSIS 

The primary structure of protein (i.e. amino acid sequence) dictates high-level protein structures (secondary, tertiary and quaternary structures) and determines their chemical 

Separation and purification of individual peptide chains from proteins containing multiple chains. 

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

Fig. 4-8 Stylized representations of protein structures in which a helices are represented as coiled ribbons and p strands are represented by arrows pointing in the N — C direction, p proteins contain predominantly /3-sheet structure (e.g., retinol binding protein and the antigen binding fragment of antibodies) while a proteins contain predominantly a helices (e.g., myoglobin), alp proteins contain a mixture of a helix and p sheet (e.g., triosephosphate isomerase).

It should be noted that most of the mentioned representations of protein structure imply that the protein remains rigid during the docking process. As a matter of fact, docking under the assumption of a rigid protein is still common practice in standard applications. Although an acceptable simplification unda certain circumstances, it can represent a serious limitation if only unbound protein structures are available. As a consequence,the inclusion of protein flexibility in the docking process is an active area of research, and a separate section is dedicated to this issue (cf. Section 3.2.1). 

Figures 4.4 and 4.5 show examples of two common types of representations of protein structures. In Figure 4.4 some of the global structural features of the myoglobin molecule are shown from the most commonly used perspective [341]. In this view the helical segments as well as the heme group are clearly recognizable. In Figure 4.5 a ribbon model of the same molecule is shown.

Figure 1. Schematic representations of protein structures (a) myohemerythrin, an a-helical protein with antiparallel helices ( >) V2 domain of an immunoglobulin, a (3-sheet protein (c) triose phosphate isomerase, a parallel a-ff protein with a central (3 barrel (d) carboxypepti-dase, a parallel a- 3 protein with a central ( -sheet structure (e)para-hydroxybenzoate hydrolase, a complex protein structure with more than one domain. (From Ref. S3 courtesy of J. Richardson.)...

Figure 3 Distribution of virtual (C — C —C ) bond angles vs. virtual (Cq —C — C -CJdi hedral angles using simplified representations of protein structure. The actual geometries of the 72 proteins listed in ref. (70) are plotted as dots, (a) Open circles are available lattice geometries for a self-avoiding knight s walk on a cubic lattice. Conformations with three collinear atoms are omitted, (b) Similar to (a) for a face-centered cubic lattice with nodes at the center of each cubic face.

FIGURE 1.18 Alternative representations of protein structure. A ribbon diagram (A) and a surface representation (B) of a key protein from the immune system emphasize different aspects of structure. 

The basic problem with the fragment assembly method is the use of the least-squares superposition, which means that the proteins are being treated as rigid bodies. This may result in only a small number of equivalent positions being used to pinpoint a large part of the model, and information other than the Ca-positions in known structures is often neglected. Thus, another technique was developed to allow a more flexible representation of protein structure, both for comparison and modelling purposes. 

FIGURE 3.11 Representation of protein structure showing (a) atomic and (b) spatial arrangement of the helix. (From Roberts, J.D. and Caserio, M.C., Basic Principles of Organic Chemistry, Benjamin Book Publishers, Inc., New York, 1964.)... 

Space-Filling Assembly This is another kind of representation of protein structure of the same three proteins in Figure 18.6. The subunits are assembled looking down the cleft into the active site. The distribution of positive charge and negative charge are often expressed on the surface. Figure 18.7 shows the assemblies of these three proteins. 

FIGURE 6.10 Cartoon representations of protein structures for (a) bovine catalase (Protein Data Bank [PDB] entry SCAT) and (b) bacteriorhodopsin (PDB entry 3WJK), a proton pump similar to the human visual pigment and found in bacterial cells. In these two examples of protein molecules, we can see the amino acid chain coiled and folded into different structures. Alpha-helical structures are shown in red and beta sheets in yellow. Diagrams such as this are commonly used to depict the complex hierarchical structure of proteins. 

Figure 45 Schematic representation of protein structure at a fluid interface. 1 = flexible, random-coil proteins 2 = globular, highly structured proteins. The arrow denotes increasing protein concentration.

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