32
3D Molecular Visualization
with Protein Explorer
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Table 1
Major Websites
Website name
Location
Protein Explorer a
World Index of Molecular Visualization Resources
http://www.proteinexplorer.org
http://www.molvisindex.org
(including tutorials using Chime, dedicated to specific molecules)
PDB Lite (search interface for novices)
Protein Data Bank
http://www.pdblite.org
http://www.pdb.org
(source of all published macromolecular structure data)
Nature and Limitations of 3-D Structural Data
Cn3D (see category “Free Software”)
DeepView (SwissPDB-Viewer)
WebLab Viewer Lite
http://www.rcsb.org/pdb/
experimental_methods.html
http://www.molvisindex.org
http://www.molvisindex.org
http://www.molvisindex.org
aConsult Protein Explorer’s Help, Index and Glossary to find how to access specific features of Protein
Explorer. It is linked to Protein Explorer’s FrontDoor under About PE.
Table 2
Some Interesting Molecules and Their PDB Identification Codesa
Molecule
Identification code
Acetylcholinesterase with inhibitor
Alpha hemolysin transmembrane heptamer
Antibody (intact IgG)
Antibody Fab bound to lysozyme
Bacteriorhodopsin
Calcineurin (ser/thr phosphatase), FKBP, FK506
Calcium transporting ATPase including transmembrane
Calmodulin (NMR ensembles)
1VOT
7AHL
1IGT
1FDL
1C8R
1TCO
1EUL
1CFC (slight flexibility) or
2BBN (much flexibility)
Green fluorescent protein
1EMB
Hemoglobin, deoxy
1HGA
Hemoglobin, oxy
1HHO
Hemoglobin, sickle
1HBS
Hemolysin transmembrane (mushroom)
7AHL
HIV protease with inhibitor
1OHR
Lipase
1LPM vs 1TRH
Lysozyme, human
1LZR
Major Histocompatibility I (with virus peptide)
2VAB
Myoglobin, oxy
1MBO
Nucleosome (histones + DNA)
1AOI
Potassium channel
1BL8
Ribosome with tRNAs and mRNA
1GIX plus 1GIYb
RNA Polymerase, T7
1QLN
Transcriptional regulator, Gal4 + DNA
1D66
Transfer RNA, Phenylalanine
1TRA
Trypsin (porcine pancreatic) complexed to soybean trypsin inhibitor 1AVX
To search for other molecules see Website: http://www.pdblite.org
a (PDB
codes are case-independent: 1VOT is the same as 1vot.)
b The ribosome is too big to fit in a single PDB file when all side chains are included. A PDB file containing
only the phosphorus atoms for the rRNA, and only the alpha carbons for proteins, is available (see Website:
http://www.molvis.sdsc.edu/pdb/1gix1giy.pdb). This URL can be entered in the long slot on the FrontDoor of
Protein Explorer.
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Fig. 1. Protein Explorer’s FirstView strives to be maximally informative. The molecule shown, PDB
identification code 1D66, is the DNA-binding domain of Yeast Gal4 complexed to a 19 base pair
DNA double helix. Rotating the image with the mouse makes 3D relationships clear, difficult to
appreciate in this static screenshot. FirstView enables you to observe how many chains are in the
molecule, which are protein and which are nucleic acid, and whether disulfide bonds or ligands
(spacefilled) are present. Protein chains have been made thicker than DNA chains in this figure;
normally all chains are the same thickness and can be distinguished by color. Extensive background information is available through hyperlinks on this screen. For example, backbone traces
and simplified disulfide bond rendering are explained graphically (not shown). Clicking on any
atom reports its identification in the message box, hence protein chains can be easily distinguished
from nucleic acid chains. The arrow indicates the atom clicked for this figure. Water, currently
hidden, is shown by default (configured in Preferences), but can be shown or hidden with the
button Hide/Show Water. The window at the lower right can be closed or reopened at any time by
pressing the Molecule Information button.
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Fig. 2. The QuickViews menu system is the heart of the user-friendly power of Protein Explorer.
Select, Display, and Color menus (see Fig. 3) and buttons make it unnecessary to learn any RasMolstyle commands. However, Rasmol commands may be entered freely by those who have learned
them. Buttons include Spin, Zoom, Background (toggles between black and white), Water, Ligand,
Molecule Information, Center (clicked atom or currently selected atoms), Stereo, Slab, and Synch.
Each menu or button action automatically displays help in the left middle frame. Sometimes the help
includes submenus. In this case, there are links to make the protein surface transparent, hidden, or
solid (it is currently transparent). This image shows an inhibitor (spacefilled) bound to the catalytic
site of lipase (divergent stereo pair). The catalytic triad (ball and stick) is visible inside the transparent
surface of the protein. This screenshot is of Protein Comparator, which is identical to ProteinExplorer
except that two molecules can be compared, one above the other. All menus and buttons work on
one molecule at a time, selected by the Top — Bottom radio buttons. In this case, the same molecule
was loaded in both top and bottom positions, but is shown at different zoom levels.
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Fig. 3. QuickViews menus expanded to show all options. These menus and associated features enable sophisticated interactive visualization without learning the RasMol command language. The
paradigm for modifying the image of the molecule, adopted from RasMol, is to select a subset of
the atoms, display or render them as desired (or hide them), and color them if desired. Repeating
these three steps on different subsets of atoms produces complex displays. Choosing Clicked on the
SELECT menu changes the action of the mouse clicks to selection, rather than the default (atom
identification). Using mouse clicks facilitates selection of arbitrary subsets of atoms, residues, or
chains. (A separate window not shown, Seq3D, enables selecting arbitrary residues or ranges by
clicking on a sequence listing.) Every menu selection automatically displays help, or for color
schemes, a color key, in the left middle frame shown in Fig. 2. A section of QuickViews called
QuickViews Plus (not shown) enables Boolean operations between items on the SELECT or DISPLAY
menus (access by scrolling down in the upper left frame in Fig. 2). For example, one can select
Protein, then subtract from the selection Helices and Strands; or one can add a ball and stick rendering to a backbone rendering. Some options on the DISPLAY menu invoke complex command scripts,
notably Contacts (see Fig. 4), Cation-Pi, and Salt Br. Nevertheless, from the perspective of the user,
these are one-click operations.
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Fig. 4. The Contacts surface display. Two clicks reveal noncovalent bonding relationships across
any interface. The user selects the moiety to be surfaced, then DISPLAY Contacts. In this case,
Chain A (one of the two homodimer protein chains in the DNA-binding domain of Gal4, 1D66)
was selected, and is shown as a surface. The surface is rendered and automatically decorated with
small spheres (balls), which represent atoms close enough to appropriate atoms beneath the surface to be noncovalently bonded. Sticks are added to the balls to show all covalent bonds up to
7 Ångstroms from the surface. All portions of the structures outside the surface that are farther than
7 Å from the surface are hidden. (The DNA backbone can be shown for context using Backbones:
Show in the lower left frame.) The surface is colored by distance from the nearest atoms. Dark areas
of the surface are too distant from any atoms to be noncovalently bonded. Light areas are at distances suitable for van der Waals interactions, and magenta areas (see companion CD for color)
are close enough for hydrogen bonds or salt bridges. The finger of this member of zinc-finger
superfamily can be seen protruding upwards, where it contacts several DNA bases in the major
groove. In color (see companion CD), it is immediately apparent that the noncovalently bonded
atoms (balls) include oxygens and nitrogens, hence that the protein is recognizing a specific base
sequence. Clicking on the nucleotide base rings that include balls, from left to right (in the rearmost
chain D), reports CGG, the published recognition sequence for Gal4.
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Fig. 5. Conserved regions (dark) of the surface of the PUF translation repressor Pumilio 1 (1LB2)
revealed by Protein Explorer’s MSA3D (divergent stereo). There is little conservation on the convex
surface (top), but a large conserved patch in the concave surface of the same molecule (bottom) is
believed to bind to the 3’ untranslated region of the mRNA. A multiple protein sequence alignment
was constructed (outside of Protein Explorer) that included sequences from human, Xenopus, Drosophila, Yeast (2), Dictylostelium, and C. elegans. A 3D crystallographic structure is available for the
human sequence (1LB2). The sequence alignment (in FASTA or PIR format) was pasted into a form
box in MSA3D, the consensus requirement set to 80% for the seven aligned sequences. With one
click of a button, MSA3D produced a text listing of the alignment (not shown) assigning three colors
representing identity, similarity, and difference. The colors were then automatically applied to the
3D molecular model. (Thanks to David S. Bernstein for providing this alignment and example.)
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