More about proteins
Today we're going to extend our discussion of protein structure. This may seem far-removed from gene cloning, but it is the path to understanding the genes that we are cloning.
Continued discussion on structure
In the last lecture, I discussed the structures and properties
of the 20 amino acids, and introduced the basic structures (such as alpha helices)
found in proteins. I'm going to extend that discussion today, focusing on the surface
and internal characteristics of proteins.
Now, to learn about secondary structure, let's switch to McClure's Protein G primer which is an outstanding site.
Choose "alpha helix" from the menu at the top, and study the structure.
Try going through the exercise in which you color the hydrophobic residues green and the hydrophilic ones red. Turn the molecule so you are looking down the axis of the helix, and it will look something like this:
This may give you an idea about how proteins are assembled beyond
a secondary structure, for if the hydrophobic residues can become clustered on one
face of a helix, they can be pushed into the interior of the protein as it folds
into a tertiary structure.
Now go to the second example of a beta hairpin, and study the dihedral angles of the Lysine 50. Alpha helices in proteins are right handed, but if you look at the phi and psi angles in turn, you can see that this individual residue provides a left handed helical structure.
In that example, try setting the display and color of the hydrophobic
residues to green ("Select"/"Protein"/"Hydrophobic")
then ("Display"/"Sticks") then ("Select"/"Change
color"), and the hydrophilic residues to red, as before. Do you see any clustering
of types of R groups?
Now go to the two examples of Type 1 turns, and look at the H bond distances across the backbone.
Now go to the Patterns of Tertiary Folding link, and look at the
packing example. Look at the van der Waals radii representation showing the buried
tyrosines, leucines, tryptophans, and phenylalanines. Look at the representation
of a "pocket" for the Phe30, noticing the atoms that are in close proximity
to the phenyl ring.
|What's inside, what's outside||One important concept is that proteins fold themselves so that hydrophobic
residues tend to be buried in the interior of the protein. Does that mean there can
never be an exposed phenylalanine or isoleucine? No, they can certainly be on the
surface, but there is an energetic cost associated with having them exposed to the
water solvent. The water must "organize" around the hydrophobic residues,
and that organization bears the cost of being a decrease in disorder or entropy.
Let's look at a typical example, the protease thermolysin, using Protein Explorer. The protein databank code for this molecule is 1LNF, and I encourage you to view it and isolate the elements I describe below.
Here is an image of thermolysin, with the alpha helices colored magenta, the beta sheets colored blue, and the remaining structures colored black. The zinc ion is indicated with an arrow. There are also three visible calcium ions (gray) in the upper-left quadrant of the image.
This allows us to review these structures that we had studied using the protein G1 (see McClure's page)
We are particularly interested in how the zinc ion is chelated in the protein. If we set the histidines in space-filling format and the rest of the protein in wire-frame format, it is easy to represent the structure:
Note that there are three histidines in the vicinity, and that
the Zn ion is nestled between two nitrogens from his142 and his146.
I recommend that you repeat this exercise with the molecule 1LNF so that you can turn the model on your computer. You may also be interested in looking at the chelation of the calcium ions around residues 195-205 of thermolysin.
|Finally, here is a representation of thermolysin, with the carbon
atoms colored black, the oxygen colored red, the nitrogen colored blue. Notice how
the water molecules are distributed in the co-crystal (as shown on right in green).
The surface of the protein in solution would be covered with water, acting as hydrogen
bond donors and acceptors with the oxygen and nitrogens of the amino acids.
Department of Biology
California State University Northridge
Northridge CA 91330-8303
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