SCOP classification

Brazzein, the smallest of sweet proteins, was discovered only in 1994 (Ming and Hellekant, 1994) in Pentadiplandra brazzeana B. This protein, whose sequence contains 54-amino acid residues, is 2000 times sweeter than sucrose when compared to a 2% sucrose aqueous solution. Its taste was described as more similar to sucrose than that of thaumatin (Ming and Hellekant, 1994). As can be seen in Figure 5C, the 3D structure of brazzein, determined by NMR spectroscopy in solution at pH 5.2 (Caldwell et al., 1998), is very simple. It contains one a-helix and three strands of antiparallel )3-sheet. The structure is stabilized by four disulfide bonds, three connecting the helix to the jS-sheet. It does not resemble either that of monellin or that of thaumatin instead, it resembles those of plant y-thionins and defensins and arthropod toxins. According to the SCOP classification (Murzin et al., 1995), brazzein belongs to the Scorpion toxin-like superfamily. 

In this section we present an empirical characterization of SSE-IN properties. In order to choose our data sample, we have used the SCOP classification. We have worked with the SCOP 1.7.3 files. We have computed the measures from the section (4.2.) for the four mains classes of SCOP (see Table 7). Each class provides a broad sample guarantying more general results and avoiding fluctuations. Moreover, these four classes contain proteins of very different sizes, varying from several dozens to several thousands amino acids in SSE. The results obtained for the different classes are very similar, that is why in the rest of this section we show only the results for... 

Figure 11 Statistics of the SCOP classification of proteins. The numbers of folds, superfamilies, and families in SCOP are plotted against time , where time is the timestamp of the PDB used to generate the update of SCOP.

Automatic Structural Ahgnment against a Manual Standard the SCOP Classification of Proteins. 

SCOP Structural Classification of Proteins. Hierarchical protein structure database... 

Murzin A G, S E Brenner, T Hubbard and C Chothia 1995. SCOP A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. Journal of Molecular Biology 247 536-540. 

TJP Hubbard, B Alley, SE Brenner, AGMurzm, C Chothia. SCOP A stiaictural classification of proteins database. Nucleic Acids Res 27 254-256, 1999. 

In order to make as much data on the structure and its determination available in the databases, approaches for automated data harvesting are being developed. Structure classification schemes, as implemented for example in the SCOP, CATH, andFSSP databases, elucidate the relationship between protein folds and function and shed light on the evolution of protein domains. 

Sequence conservation is, in general, much weaker than structural conservation. There are proteins, which are clearly not related in sequence but are closely related in 3D-stmcture and fold, like heamoglobin and myoglobin, which have similar functions. In many proteins, fold elements like 4-helical bundles are repeated. Classifications of known structural folds of proteins are organized in the SCOP or CATH database see e.g., http //scop.mrc-lmb.cam.ac.uk/scop/. 

FIGURE 4-22 Organization of proteins based on motifs. Shown here are just a small number of the hundreds of known stable motifs. They are divided into four classes all a, all /3, all3, and a + /3. Structural classification data from the SCOP (Structural Classification of Proteins) database (http //scop.mrc-lmb.cam.ac.uk/scop) are also provided. The PDB identifier is the unique number given to each structure archived in the Protein Data Bank (www.rcsb.org/pdb). The a//3 barrel, shown in Figure 4-21, is another particularly common a/fS motif. 

The SCOP database is curated manually, with the objective of placing proteins in the correct evolutionary framework based on conserved structural features. Two similar enterprises, the CATH (class, architecture, topology, and homologous superfamily) and FSSP (/old classification based on structure-structure alignment of proteins) databases, make use of more automated methods and can provide additional information. 

Structural classification of proteins SCOP http //vmrw.bio.cam.ac.uk/scop/... 

A classification system, such as SCOP (Lesk and Chothia, 1984), categorizes structure domains based on secondary structural elements within a protein into a. structure (made up primarily from a helices), / structure (made up primarily from / strands), a// structure (comprised of primarily P strands alternating with a helices), and a + P structure (comprised of a mixture of isolated a helices and / strands). In this classification (Brenner et al, 1996 Lesk, 1991), only the core of the domain is considered. Therefore, it is possible for an all-a structure to have very small amount of p strand outside the a-helical core. Similarly, an all-/ protein may have a small presence of a or 310 helix. The SCOP (http //scop.mrc-lmb.cam.ac.uk/scop/) can be summarized as follows ... 

PALI (Phylogeny and Alignment of Homologous Protein Domains) Database. The PALI (v 2.6) database provides three-dimensional structure-based sequence alignments for homologous proteins of known three-dimensional structure (24-26). The protein families have been derived from the SCOP (Structural Classification of Proteins) database (27). There are 2,518 protein families, and using more than one sequence as reference, 37,986 profiles have been generated. 

Murzin AG, Brennerm SE, Hubbard T et al (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247 536-540... 

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