Chemistry Department University of Southern Maine
Links To Files Used In Biochemistry Class (CHY 361-363)
Topic: Three-Dimensional Structure of Proteins
For graphics from other topics, see Topics List.
Set your browser to use RasMol for PDB files and RasMol scripts: See Configuring Netscape.
Molecules to Explore Cytochrome b5
Cytochrome b5 is an electron-carrier protein found in the liver, where it appears to be involved in redox reactions that detoxify foreign substances. Although cytochrome b5 is a small protein, it contains most of the features you will find in the most complex proteins, including helices, sheets, turns, and a prosthetic group (iron-heme). Exploring this little protein is a good way to solidify your understanding of many aspects of proteinstructure. For this, perhaps your first protein exploration, I have added some extra help in the form of RasMol scripts that highlight specific parts of the molecule.
If you plan to use the scripts, you must have a copy of RasMol already running on your desktop, before you click to download the structure file. From the structure file or any script, you can put your knowledge of RasMol to use by displaying and exploring additional parts of the molecule.
If you are not a RasMol user, you can explore the structure file with any molecular viewer.
First, obtain the structure file by clicking here: 3b5c.pdb
Second, click on any of the script names below to download and run a script.
NOTE: If RasMol does not execute the script (and I can't figure out why it does on some computers and doesn't on others), type script followed by the script name on the RasMol command line. For example, for the first script, you would type script cb5-01.spt. Then press the return key, and RasMol should execute the script.
ANOTHER NOTE: If the model swings about wildly when you try to rotate it, enter the command set picking center on the RasMol command line, and press return. Then click on an atom near the center of the display. After this action, the model will rotate around the selected atom. It is handy to leave picking set this way when downloading a seris of scripts. To reset RasMol for identifying picked atoms, use the command set picking ident.
1. Cytochrome b5 backbone, colored to highlight secondary structure: cb5-01.spt
2. Backbone with one alpha helix shown in green: cb5-02.spt
3. Detail of mainchain atoms in the alpha helix: cb5-03.spt
4. Backbone with beta sheet highlighted in yellow: cb5-04.spt
5. Detail of mainchain atoms in the sheet: cb5-05.spt
6.Backbone with a beta turn shown in green: cb5-06.spt
7. Detail of mainchain atoms in the beta turn: cb5-07.spt
8. View showing the heme prosthetic group of cytochrome b5: cb5-08.spt
9. Positive (orange), negative (cyan), and polar (green) side chains (note the most are exposed at the surface of the molecule: cb5-09.spt
10.Hydrophobic side chains shown in yellow (note that most are buried within the molecule: cb5-10.spt
11. Spacefilling model with side chains colored as in scripts 9 and 10, mainchain in CPK colors, and heme in white with purple oxygens, blue nitrogens (hidden), and red-orange iron (hidden). After loading this view, type "slab" <return> on the command line. Then hold down the "control" key and drag the mouse up and down to slice through the view. Note the preponderance of hydrophobic groups in contact with the hydrophobic heme: cb5-11.spt
12. Closeup of heme and the two histidine ligands: cb5-12.spt
13. More details at the heme pocket. Zoom out to see the full view: cb5-13.spt
Malate Dehydrogenase Example of dimeric protein and of domains.
Malate dehydrogenase (MDH) is an enzyme that interconverts malate and oxaloacetate, using the NAD+/NADH redox couple. This particular MDH is dimeric in solution. Each monomer contains two 2 domains. The N-terminal, or first 1st, domain binds NAD+ or NADH. The second 2nd domain binds malate or oxaloacetate. The first 1st domain is a typical dinucleotide-binding domain.
Click here for malate dehydrogenase: 1bmd.pdb NOTE: This is a large file (450 kb) and will take a few minutes to download.
After RasMol has opened 1bmd.pdb, click on these script files to download and run scripts. While these scripts download rapidly, some of them require several seconds to execute, during which time RasMol will present you with a black screen. Be patient -- the view will eventually appear. If they download but do not execute, see the NOTE above.
1. Malate dehydrogenase backbone, colored to distinguish the two monomers of this dimeric enzyme: mdh-01.spt
2. One monomer, colored to distinguish the two domains. First domain is green, second is red: mdh-02.spt
3. First domain of the monomer, colored to show that the first domain is made up of two similar subdomains: mdh-03.spt
4. One beta-alpha-beta fold, in red, in the first domain: mdh-04.spt
5. First domain, showing detail of the alpha helix that partially stabilizes phosphate charge in NAD: mdh-05.spt . Notice that the helix dipole is oriented with its positive end down on one of the negatively charge phosphates. This is a common feature in nucleotide-binding domains.
Myoglobin Click here for oxymyoglobin: 1mbo.pdb
Hemoglobin
Click here for deoxyhemoglobin: bio3hhb.pdb
Click here for oxyhemoglobin: bio1hho.pdb
More about heme-iron in the Bioinorganic Chemistry Gallery.
NOTES
· These specially prepared PDB files contain coordinates of the full tetramer. The standard PDB files for hemoglobin contain only the coordinates of an alpha/beta dimer. You can find complete models of other oligomeric proteins in the PDB's List of Prepared Biologically Functional Molecules.
· Compare the shapes of the hemes in the deoxy and oxy forms. Note in particular the position of the iron (II) ion with respect to the plane of the heme.
· Compare the ligands to iron in the two forms. One ligand you might overlook in deoxyhemoglobin is a water molecule.
Structural Comparisons: Deoxy- Versus Oxyhemoglobin (For SwissPdbViewers Only)
To use these views, you must configure your browser to use SwissPdbViewer for files of MIME type chemical/x-pdb, with suffix pdb. See Configuring Netscape.
If you are not familiar with SwissPdbViewer, see Which Modeling Program Is For You? and this Tutorial.
Hemoglobin Beta Subunit
First, here are files of the beta subunit. Click to download and open the first file in SwissPdbViewer, and then return to this page and click to download and open the second file. Superimpose them and study the changes that occur when oxygen binds to hemoglobin:
Deoxyhemoglobin, beta subunit: 3hhbBeta.pdb
Oxyhemoglobin, beta subunit: 1hhoBeta.pdb
After loading and superimposing, turn the two models on and off in quick succession to see the changes that occur on oxygenation and deoxygenation. This is called blinking.
Here's how to blink:
1. With both models visible, click Visible on the Control Panel to make the top model invisible
2. Hold the mouse pointer over the Visible button on the control panel, and hold a finger on the tab key.
3. Click Visible, press tab, click Visible.
4. Each time you repeat this three-step move, you turn one model on and the other off.
Hemoglobin Heme Region
Here are comparision files of the heme region, beta subunit only. Download the two files in succession. Do not move the first model before loading the second, and you should find them already superimposed. (If not, select Prefs: General Preferences and turn off Center Molecule Upon Loading. Then reload both files.)
Blink between the two models as described above for the beta subunits. The movement of the proximal histidine (His92), following the Fe2+ ion as it moves into the heme plane, is thought to trigger the conformational changes increase oxygen affinity in the other three subunits. Thus this motion is proposed to be the basis of cooperativity in hemoglobin.
Deoxyhemoglobin, beta subunit, heme region: 3hhbBetaHem.pdb
Oxyhemoglobin, beta subunit, heme region: 1hhoBetaHem.pdb
Hemoglobin Asp94/His146 Region
Here are comparison files of a salt bridge that breaks when oxygen binds to hemoglobin. Use them as described above for the heme-region files.
Blink between the two models to see the formation and breakage of the salt bridge. Breakage of this salt bridge is thought to be the basis of the Bohr effect: the release of H+ upon oxygen binding. Breakage of the salt bridge makes the imidazole side chain of His146 more acidic, and leads to dissociation of a proton.
Deoxyhemoglobin, beta subunit, Asp94/His146 region: 3hhbBetaHD.pdb
Oxyhemoglobin, beta subunit, Asp94/His146 region: 1hhoBetaHD.pdb
To Topics List. To Biochemistry Resources. HOME
