Display of 3D Structures with Molecular Graphics Programs

For the 3D view of ISIS/Draw, ACD/3D Viewer Add-in can be installed. Retrieve ACD/3D Viewer for ISIS/Draw from http://www.acdlabs.com/downloar/ download.cgi and installed it as an Add-in according to instructions. To view 3D structure which is opened/sketched on the ISIS/Draw window, select ACD/3D Viewer tool from Object menu to open ACD/3D Viewer window and subsequent display of the 3D structure. The 3D structure can be optimized and can be saved only in .s3d format, which is not recognizable by other modeling packages.

The 2D structures of ISIS draw can be transformed into the 3D structures by WebLab Viewer Lite, which can be downloaded free for academic use from Accelrys Inc. at http://www.accelrys.com/viewer/viewlite/index.html. Select Download View-

Figure 4.14. Conversion of 2D structure into 3D structure. The 2D structure file from ISIS draw (stanley.skc) is converted into the 3D structure with WebLab Viewer Lite. It should be noted that the atomic coordinate file does not contain ATOM columns with residue ID.

lite to register and download. Open the file by selecting MDL (*.skc); the 2D structure (e.g., hexapeptide, stanley.skc) is converted into the 3D structure (Figure 4.14) whose coordinate file can be saved as struname.pdb (e.g., stanley.pdb).

Alternately, the commercial molecular modeling software programs such as ChemOffice (http://www.camsoft.com) can be used. The ISIS draw in sketch format (struname.skc) is first converted to ChemDraw format (struname.cdx), which is then transformed into 3D structure (struname.c3d) with Chem 3D (Chapter 14) and saved as PDB format (struname.pdb).

The common atomic coordinate files for 3D structure in biochemistry is PDB format. The pdb files of polysaccharides, proteins, and nucleic acids can be retrieved from the Protein Data Bank at RCSB (http://www.rcsb.org/pdb/). On the home page (Figure 4.15), enter PDB ID (check the box ''query by PDB id only'') or keywords (check the box ''match exact word'') and click Find a structure button. Alternatively, initiate search/retrieval by selecting SearchLite. On the query page, enter the keyword (e.g., the name of ligand or biomacromolecule) and click Search button. Select the desired entry from the list of hits to access Summary information of the selected molecule. From the Summary information, select Download/Display file and then PDB Text and PDB noncompression format to retrieve the pdb file. In order to display 3D structure online, choose View structure followed by selecting one of 3D display options. The display can be saved in .jpg or . gif image format.

Most of molecular modeling software programs accept the pdb files (struname.pdb). RasMol, which is one of the most widely used molecular graphics freeware, can be downloaded from http://www.umass.edu/microbio/rasmol/

index2.htm. In addition to PDB (struname.pdb or struname.ent) file, RasMol also read Alchemy, Sybtk MOL2, MDL mol, CHARMm, and MOPAC files. Launch RasMol (double click rswin.exe or rw32b2a.exe) to open the display window. Open the pdb file from File menu. The 3D structure can be displayed as wireframe, backbone, sticks, spacefill, ball and stick, ribbons, strands and cartoons (Figure 4.16). The display can be exported as bmp, gif, epsf, ppm, and rast graphics.

KineMage (kinetic image) is an interactive 3D structure illustration software that can be downloaded from http://orca.st.usm.edu/ ~ rbateman/kinemage/. It is adapted for the structure representation of biological molecules by many biochemical textbooks. The program consists of two components: PREKIN and MAGE. The PREKIN program interprets struname.pdb file to kinemage struname.kin file that is then displayed and manipulated with the MAGE program. To start the PREKIN program, click Proceed to enter an output file name. This opens a dialog box, ''Starting ranges.'' Accepting the default (Backbone browsing script) saves the script producing Ca, disulfides for all subunits in the file to struname.kin. To start the MERGE program, click Proceed and select Open new file from File menu to open struname.kin with three windows (caption, display, and text). The 3D structure with connected series of alpha carbons is shown in the display window. To highlight the secondary structures, choose Selection of build-in scripts from the dialog box, ''Starting ranges,'' to open Build-in scripts box. Select ribbon: HELIX, SHEET from pdb to save as ribbon.kin. The MERGE program opens ribbon.kin as shown in Figure 4.17.

Cn3D is a molecular graphics program that interprets structure files in MMDB (ASN.1) format (struname.val or struname.cgi) of Entrez/MMDB (Wang et al.,

Figure 4.15. Home page of PDB at Research Collaboratory for Structural Bioinformatics.
Alcohol Dehydrogenase Viewerlite
Figure 4.16. Graphic display of 3D structure with RasMol. The display shows the 3D structure of liver alcohol dehydrogenase complex (6ADH.pdb) with two subunits and bound NAD + . The protein molecule is visualized with RasMenu.
Egg Lysozyme
Figure 4.17. Graphic display of KineMage in ribbon representation. The Ca chain of hen's egg-white lysozyme (1LYZ.kin derived from 1LYZ.pdb) is displayed in ribbons showing secondary structure features.
Grafikprogramme

Figure 4.18. Graphic display of macromolecular interaction with Cn3D. The display window of Cn3D illustrates the 3D structure of Zn finger peptide fragments (secondary structure features) bound to the duplex oligonucleotides (brown backbone). Zinc atoms are depicted as spheres. The alignment window shows the amino acid sequence depicting the secondary structures (blue helices and arrows for a-helical and ^-strand structures, respectively) and interacting (thin brown arrows) residues. The structure file, 1A1K.val, is derived from lAAY.pdb.

Figure 4.18. Graphic display of macromolecular interaction with Cn3D. The display window of Cn3D illustrates the 3D structure of Zn finger peptide fragments (secondary structure features) bound to the duplex oligonucleotides (brown backbone). Zinc atoms are depicted as spheres. The alignment window shows the amino acid sequence depicting the secondary structures (blue helices and arrows for a-helical and ^-strand structures, respectively) and interacting (thin brown arrows) residues. The structure file, 1A1K.val, is derived from lAAY.pdb.

2002). Cn3D can be accessed online from Entrez at http://www.ncbi.nlm.nih.gov/ Entrez or downloaded from http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.html to be installed and used locally. This program accepts the coordinate file in MMDB ASN.1 format (*.val or *.cgi) but can be saved as PDB format (*.pdb) or KineMage format (*.kin). It is a structure-sequence interactive program. In addition to structure view in the Graphic window, Cn3D provides the sequence view in the Sequence window which can be activated via View — Sequence Window (Figure 4.18). This enables the user to view the structure and sequence interactively. Select the region of protein molecule in the structure view by double clicking of the mouse, and both the region in the Graphic window and the amino acid residue(s) in the Sequence window are highlighted (yellow) and vice versa. Using this tool, it is possible to map the interaction sites between structure and sequence. The view menu of the Graphic window also provides an option for Animation, and the Sequence window offers options for alignment (Align menu). The style menu enables the user to display the structure in secondary structure, wireframe, neighbor, tabular, spacefill or ball-and-stick modes (Figure 4.11).

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