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Three-dimensional structural data bases

The Protein Data Bank (PDB http //www.pdb.org) is the worldwide repository of three-dimensional structural data of biological macromolecules, such as proteins and nucleic acids (Berman et al. 2003). The Protein Data Bank uses several text file-based formats for data deposition, processing, and archiving. The oldest of these is the Protein Data Bank format (Bernstein 1977), which is used both for deposition and for retrieval of results. It is a plain-text format whose main part, a so-called primary structure section, contains the atomic coordinates within the sequence of residues (e.g., nucleotides or amino acids) in each chain of the macromolecule. Embedded in these records are chain identifiers and sequence numbers that allow other records to reference parts of the sequence. Apart from structural data, the PDB format also allows for storing of various metadata such as bibliographic data, experimental conditions, additional stereochemistry information, and so on. However, the amount of metadata types available is rather limited owing to the age of the PDB format and to its relatively strict syntax rules. [Pg.91]

As described in Section I. C, NMR experiments can provide a characterization of polypeptide conformation even when the chain is flexibly disordered and does not adopt a discrete set of three-dimensional structures. Thus, based on data corresponding to those for bPrP in Figures 6 and 7 (Lopez-Garcia et al, 2000), it was demonstrated that the N-termi-nal half of the intact polypeptide chain forms a flexible tail in mPrP (Riek et al, 1997), shPrP (Donne et al, 1997), and hPrP (Zahn et al,... [Pg.73]

Empirical statistical methods, which are based upon data generated from studying proteins of known three-dimensional structure and correlation of such proteins primary amino acid sequences with structural features. [Pg.29]

Complete structural analysis requires mass spectral and NMR data as well as chemical degradation and analysis of the chirality of the constituent amino acids, determination of the mode of linkage of lysine (a- or s-), the size of the cyclopeptide or cyclodepsipeptide ring, etc. (37). In some cases sttuctures have been proposed based only on mass spectral data. Difficulties arising in this approach were discussed (44). To determine the three-dimensional structure an X-ray... [Pg.5]

Until now, the determination of three-dimensional structures of oligosaccharides in solution was based primarily on proton-proton distance information obtained from n.O.e. data. Here, we discuss the application of three-bond proton-carbon coupling constants. [Pg.169]

The first surprise was that these molecules are much longer than seems necessary for the formation of adapters. In addition, 10-20% of their bases are modified greatly from their original form.171 Another surprise was that the anticodons are not all made up of "standard" bases. Thus, hypoxanthine (whose nucleoside is inosine) occurs in some anticodons. Conventional "cloverleaf" representations of tRNA, which display their secondary structures, are shown in Figs. 5-30 and 29-7. However, the molecules usually have an L shape rather than a cloverleaf form (Figs. 5-31 and 29-6),172 and the L form is essential for functioning in protein synthesis as indicated by X-ray and other data.173 Three-dimensional structures, now determined for several different tRNAs,174 175 are all very similar. Structures in solution are also thought to be... [Pg.1687]

Catalyst [67] was launched 1992 by BioCAD (now Accelrys) as a tool for automated pharmacophore pattern recognition in a collection of compounds based on chemical features correlated with three-dimensional structure and biological activity data. [Pg.28]

Figure 12. Three-dimensional structures of Na+-K+-ATPase and Ca2+-ATPase based on image reconstruction analysis of electron microscopic data obtained from two-dimensional membrane crystals, (a). Na+-K+-ATPase molecule consisting of one a-subunit and one p-subunit. The horizontal arrows indicate a tentative location of the membrane surfaces (upper arrow cytoplasmic surface lower arrow extracellular surface suggested membrane thickness 39 A). Data from Hebert et al., 1988. (b). Ca2+-ATPase molecule consisting only of a catalytic subunit. A tentative location of the transmembrane helices (M1-M10) is indicated. The cytoplasmic part (head) is pointing upwards. In this study, the membrane (sarcoplasmic reticulum) was found to be only 32 A thick (surfaces indicated by shaded areas). Modified from Toyoshima et al., 1993. [Pg.25]


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Data bases

Data structure

Structural data

Structured data

Three structures

Three-dimensional data

Three-dimensional structure

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