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Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins - Baxevanis A.D.

Baxevanis A.D. Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins - New York, 2001. - 493 p.
ISBN 0-471-22392-1
Download (direct link): bioinformaticsapractic2001.pdf
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Because the protein structure record 1BN1 has three barnase molecules in the crystallographic unit, the PDB file has been hand-edited using a text editor to delete the superfluous chains. Editing data files is an accepted and widespread practice in three-dimensional molecular structure software, forcing the three-dimensional structure viewer to show what the user wants. In this case, the crystallographic data
Figure 5.5. A constellation of viewing alternatives using RasMol with a portion of the barnase structure 1BN1 (Buckle et al., 1993). 1BN1 has three barnase molecules in the asymmetric unit. For this figure, the author edited the PDB file to remove two extra barnase molecules to make the images. Like most crystal structures, 1BN1 has no hydrogen locations. (a) Barnase in CPK coloring (element-based coloring) in a wire-frame representation. (b) Barnase in a space-filling representation. (c) Barnase in an a-carbon backbone representation, colored by residue type. The command line was used to select all the tryptophan residues, render them with ''sticks,'' color them purple, and show a dot surface representation. (d) Barnase in a cartoon format showing secondary structure, a-helices in red; f3-strands in yellow. Note that in all cases the default atom or residue coloring schemes used are at the discretion of the author of the software. (See color plate.)
recorded in the three-dimensional structure does not represent the functional biological unit. In our example, the molecule barnase is a monomer; however, we have three molecules in the crystallographic unit. In our other example, 3TS1 (Brick et al., 1989) (Fig. 5.3), the molecule is a dimer, but only one of the symmetric subunits is recorded in the PDB file.
The wire-frame image in Figure 5.5a clearly shows the chemistry of the barnase structure, and we can easily trace of the sequence of barnase on the image of its biopolymer in an interactive computer display. The space-filling model in Figure
5.5b gives a good indication of the size and surface of the biopolymer, yet it is difficult to follow the details of chemistry and bonding in this representation. The composite illustration in Figure 5.5c shows an a-carbon backbone in a typical pseudo-structure representation. The lines drawn are not actual chemical bonds, but they guide us along the path made by the a-carbons of the protein backbone. These are also called ‘‘virtual bonds.’’ The purple tryptophan side chains have been selected and drawn together with a dot surface. This composite illustration highlights the volume taken up by the three tryptophan side chains in three hydrophobic core regions of barnase, while effectively hiding most of the structure’s details.
The ribbon model in Figure 5.5d shows the organization of the structural path of the secondary structure elements of the protein chain (a-helix and ^-sheet regions). This representation is very often used, with the arrowheads indicating the N-to-C-terminal direction of the secondary structure elements, and is most effective for identifying secondary structures within complex topologies.
The variety of information conveyed by the different views in Figure 5.5 illustrates the need to visualize three-dimensional biopolymer structure data in unique ways that are not common to other three-dimensional graphics applications. This requirement often precludes the effective use of software from the “macroscopic world,’’ such as computer-aided design (CAD) or virtual reality modeling language (VRML) packages.
Picture the Data: Populations, Degeneracy, and Dynamics
Both X-ray and NMR techniques infer three-dimensional structure from a synchronized population of molecules—synchronized in space as an ordered crystal lattice or synchronized in behavior as nuclear spin states are organized by an external magnetic field. In both cases, information is gathered from the population as a whole. The coordinate (x, y, z) locations of atoms in a structure are derived using numerical methods. These fit the expected chemical graph of the sample into the three-dimensional data derived from the experimental data. The expected chemical graph can include a mixture of biopolymer sequence-derived information as well as the chemical graph of any other known small molecules present in the sample, such as substrates, prosthetic groups, and ions.
One somewhat unexpected result of the use of molecular populations is the assignment of degenerate coordinates in a database record, i.e., more than one coordinate location for a single atom in the chemical graph. This is recorded when the population of molecules has observable conformational heterogeneity.
NMR Models and Ensembles
Figure 5.6 (see also color plate) presents four three-dimensional structures (images on the left were determined using X-ray crystallography and the right using NMR). The NMR structures on the left appear ‘‘fuzzy.’’ In fact, there are several different, complete structures piled one on top of another in these images. Each structure is referred to as a model, and the set of models is an ensemble. Each model in the ensemble is a chirally correct, plausible structure that fits the underlying NMR data as well as any other model in the ensemble.
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