Protein RASMOL

Figure C2.5.5. Native stmcture of acyl-coenzyme A binding protein (first NMR stmcture out of 29 deposited to PDB). The figure was created using RasMol 2.6 [8],...

Figure 12 ModBase, a database of comparative protein stracture models. Screenshots of the following ModBase panels are shown A form for searching for the models of a given protein, summary of the search results, summary of the models of a given protein, details about a single model, alignment on which a given model was based, 3D model displayed by RASMOL [237], and a model evaluation by the Prosall profile [217],...

Visualization software allows the user to display molecular structures imported from databases or other software programs. Chime, RasMol, and Protein Explorer programs are available at the websites listed below for Windows operating PCs and Macintosh PowerPC computers. 

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB at http //www.rcsb.org/pdb/) is the online source for X-ray and NMR structural data. Many software programs mentioned in Section 3.12 include the facility to visualize imported data however, two free software programs operate well in this regard. These are RasMol and Chime, described below. 

Protein Explorer, a free RasMol and Chime derivative with extended capabilities, is available at http //www.umass.edu/microbio/chime/explorer/. The program allows the user to visualize macromolecular structure in relation to function. 

Fig. 2. An example of a complex multidomain protein that includes both domain concatenation and intercalation. (A) See color insert. RASMOL view of phosphotransferase pyruvate kinase (pdb entry lpkn) colored to show the three identifiable domains. Blue is the j3 barrel regulatory domain, orange is an eightfold a/fi barrel, the catalytic substrate binding domain, and green is a central /3, a/(B nucleotide binding domain. Not displayed is the leader subsequence composed of a random coil and short helix. (B) Linear order along the sequence of these components.

Rasmol It was one of the first Protein Databank (PDB) compatible viewers available as freeware. Upgrades have now been stopped, but the program is still widely available. Versions exist for both PC and Mac. 

Protein explorer This program is the expanded version of Rasmol and works very well. It is available at http //proteinexplorer.org and has better mouse control than Rasmol. 

Figure 10.4. The D. vulgaris Rbo dimer (Coehlo et al. 1997). Spheres, iron atoms in centers I and II. The model was generated via RASMOL (Sayle and MUner-White 1995) and coordinates from IDFX in the Protein Databank.

Figure 10.6. Structural features of D. vulgaris Rbr (deMare et al. 1996). A, Rbr subunit with protein backbone and iron atoms (spheres). B, Diiron-oxo site with amino acid side chain ligands. Models generated via RASMOL (Sayle and Milner-White 1995) and coordinates from IRYT in the Protein Databank.

RasMol (RasMac) Molecular graphics for proteins http //www.umass.edu/microbio/rasmol/... 

Another useful structure tool is RasMol (or RasMac). This will allow you to view the detailed structure of a protein and rotate it on coordinates so you can see it from all perspectives. A hyperlink to RasMol is present under the View Structure function just above Chime. You may need to study RasMol instructions provided under Help, or you may use a Ra.s Mol tutorial listed in Table El.2. Another useful protein viewer is tin-Swiss-Protein Pdv Viewer (Table El.2). BLAST is an advanced sequence similarity tool available at NCBI. To access this, go to the NCBI home page (www.ncbi.nlm.nih.gov) and click on BLAST. Then click on Basic BLAST search to obtain a dialogue box into which you may type the amino acid sequence of human a-lactalbumin. This process may be stream lined by downloading the amino acid sequence in FASTA format into a file and transferring the fde into the BLAST dialogue box. BLAST will provide a list of proteins with sequences similar to the one entered. 

BLAST Chime Entrez (NCBI) FASTA GenBank (NCBI) Molecules R Us RasMol (Ras Mac) SRS (EMBL) Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences Provides coordinates for protein 3D structure and manipulation Provides coordinates for protein 3D structure and manipulation Sequence retrieval system for cross referencing databases... 

Protein Explorer is a knowledge base with introductory information on many topics about protein structure, such as the origins and limitations of 3D protein structure data, specific oligomers vs. crystal contacts, hydrogen bonds, cahon-pl interactions, etc. Protein Explorer is more user-friendly than the comparable software RASMOL, also available on servers such as ExPASy. 

Figure 4.11. Graphic representations of protein 3D structure. Three-dimensional graphics of hen s egg-white lysozyme as visualized with RasMol (first and second rows, ILYZ.pdb) and Cn3D (third row, ILYZ.val) are shown from left to right (color type) in wireframe (atom), spacefill (atom), dots (residue), backbone (residue), ribbons (secondary structure), strands (secondary structure), secondary structure (secondary structure), ball-and-stick (residue), and tubular (domain) representations.

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.

Retrieve a protein pdb hie and visualize its 3D structure with RasMol in different representations (Display menu). Identify the structural features or characteristics for which each display is best illustrative. 

Figure 12.3. MMDB Structure summary. A search for the DNA protein complex from MMDB returns a list of hits from which human topoisomerase l-DNA complex (1EJ9) is selected. The structure summary offers options for viewing and saving the structure via Cn3D, (Kine)Mage, or RasMol (PDB) as well as Sequence neighbors or Structure neighbors.

The 3D-PSSM (Kelley et ah, 2000) server at http //www.bmm.icnet.uk/ 3dpssm/ offers online protein fold recognition. On the submission form, enter your e-mail address and a one-line description of the query protein, then paste the query sequence into the sequence box and click the Submit button. The query sequence is used to search the Fold library for homologues. You will be informed of the URL where the result is located for 4 days. The output includes a summary table (hits with statistics models that can be viewed with RasMol classifications and links) and fold recognition by 3D-PSSM with a printout as exemplified in Figure 12.13. The alignment displays consensus sequence, secondary structures (C for coil, E for extended, and H for helix), and core score (0 for exterior to 9 for interior core). 

Protein explorer is one of the most widely used visualization tools for protein structures. Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. Protein explorer is easy to use, free, and widely used. It can be used be novice users as well as experts. The RasMol website has been visited by over 250,000people from 115 countries. 

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