Biophys Tools Hist Med Rsrch

A quick tour of the PDB, looking at Zinc Fingers and Myeloperoxidase, or MPO→ MPO is that enzyme that can help kill bacteria by leading to the production of HOCl, hypochlorous acid. But MPO may also have effects on HDL, the “good cholesterol ” (or sometimes good). And the HOCl may contribute to plaque rupture.

Science in progress

Part 1: Pulling up an image Part 2: Changing image, looking for SS bonds, making measurements (p. 12 +) ↑ sulfur-sulfur

Physics 3750. How-to material for part of Assignment 2 Due February 20, 2018

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Part 1. Pulling up an image of a protein you want to measure. First, search for “About Molecule of the Month pdb”

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Actually this image is from January, 2013

Last month would have been JR’s 99th birthday

But the following material has been updated

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Here it is :

Or …You can get there directly through this link: http://pdb101.rcsb.org/motm/motm-about

http://pdb101.rcsb.org/motm/motm-about

Now Click on By Date … or By Category or By Title

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Clicking By Date brings us to a collection of molecules arranged by year and month

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Look through the collection, click on a few molecules if you’d like, and choose one that interests you. Then, if no one has taken it first, sign up for it on Blackboard

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For instance, I chose Zinc Fingers, from March, 2007.

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Clicking on a protein should take you to a page that at the top might look like this. Now look down the page for a link, at the words “PDB entry —-”

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Here, for example, there are three links, way down in the Sticky Fingers section:

PDB entry 2hgh, PDB entry 1un6, and PDB entry 1tf6

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You can use Find PDB entry to locate these

Now if we click on the PDB entry link, 1tf6 . . .

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… That takes us to a page that looks like this. (End of part 1)

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Part II Go to the page of the protein that you want to investigate. (This time I chose myeloperoxidase 1MHL. MPO is that enzyme that helps kill bacteria by producing HOCl ↑). Note that Molecular Weight (‘Total Structure Weight’) is down under Resolution is under ‘Experimental Data Snapshot’

Macromolecule Content

Macromolecule content

Hypo- chlorous

Acid

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■

Part II The next step is to Click on 3D View Structure, over here

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An image of the protein appears. Now switch from NGL to JSmol (This image ↓ is interesting, but distances can’t be measured on it)

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Switching just means clicking on “Select a different viewer” to go from NGL to JSmol

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Another image of the protein appears. This image can be rotated, enlarged, etc.

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Here is a view obtained by rotating the image. Now, if you’d like to, you might try changing Secondary Structures to Amino Acids. The different colors show all the amino acids that make up this particular protein

Unfortunately this part is not

always working

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When it does work, clicking on By Amino Acid gives an image colored like this.

Key to the colors of a few of the amino acids in ↑ MPO Lys & Arg (positive) Asp & Glu (negative) Val (neutral)

Cys (neutral)

By Amino Acid

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disulfide

To see the bonds between sulfur atoms that help shape the molecule, click on SS bonds

Also called disulfide bonds or disulfide bridges

Sulfur- Sulfur Bonds

By Amino Acid

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■ NOTES ON SULFUR BONDS

Clicking on SS Bonds gives us a page like this. Look for some tiny golden lines. They are between amino acids* that contain sulfur. These “SS bonds” help bend the molecule around.

* Sulfur is contained in the amino acid cysteine This part is not

always working either

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A second example: sulfur bonds, or disulfide bonds in

Albumin (Human Serum Albumin, HSA)

HSA transports fats (specifically, free fatty acids) through the bloodstream. The sulfur bonds in albumin help shape the molecule to allow it to transport fats. (Also important is the way other amino acids interact with water: are they hydrophilic or hydrophobic?)

Here is a picture of HSA ▼ carrying fats. And here are a few locations of cysteine, an amino acid with sulfur in it (yellow areas):

Cys

↑ General image of sulfur bonds helping to shape a protein Source: Wiki, Ju

Both images from Protein Data Bank ( Cys added)

Cys

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Finally, rest the cursor on one point in the molecule. Double click. Move the cursor to another point. Double click. A distance number should appear.

So the measurement part is mostly done! Except that sometimes …

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■ NOTES ON MEASURING THE PROTEIN

Sometimes the mechanism doesn’t seem to work. In such a case, you might try putting the cursor carefully on some part of the protein molecule, and letting it rest there a moment .

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A name of an amino acid should appear. In this case, it’s ALA, for Alanine.

Double click. The cursor should change to a large + sign. Next, move the + to some other part of the molecule.

←ALA: alanine

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A faint pink line should follow the as you move it

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Then rest the carefully on some other part of the molecule. It should again tell you the amino acid you have reached. Double click.

←PRO: proline

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The line should go black (or white, if you’re on a black background.) The distance number, 52.5 Ångstroms in this case, should go black too. And now, the measurement of one part of this protein is done. . . .

52.52 Å = 5.25 nm

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… Except that sometimes, on some computers , it seems that the mechanism can still be cranky. For example, on one old computer , I could not obtain distances until I right-clicked, then clicked on Measurements, and then clicked on Click for distance measurements

After that, the distance-measuring went according to plan. (I was skeptical, but tried this way 4 times, and 4 times the normal way. Only this way worked. Aggravating machine.)

Fortunately, the computers in the computer lab all seem to be up-to-date. So please remember to give yourself a little extra time, in case of cranky machinery (possibly requiring you to use other equipment) or difficulties at site.

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52.52 Å

Export 3D 33 Image Remember, your image has to have measurements printed out

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■ NOTES ON DOWNLOADING THE IMAGE of the molecule and measurements

To download, begin by right-clicking somewhere on the page

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Click on File, then on Export and finally on Export PNG Image The menu boxes below appear.