Proteins are Dynamic & Cool

These pictures are different renderings of the same molecule. It’s called the “BK Channel,” which is short for “Big Potassium (seriously) Channel.”  (K+ is the symbol for potassium ion). It’s called that because it’s the large-conductance potassium ion transporter and it’s located in the membranes of neurons — it’s job is to return the neuron to a resting potential by transporting positively charged K+ ions back into the cell that had been released during an axon “firing” an action potential. It’s essentially a component in a battery-recharge system that allows neurons to be in a state capable of doing one of its functions. The protein itself is just one of those molecules (different colors) and it self-assembles into these groups of 4 identical subunits.

kcnma1s
Different renderings of the BK Channel. It is composed of four identical subunits that assemble in the membranes of neurons. The region that is missing as a result of exposure to Methamphetamine and/or inflammatory factors is highlighted in yellow.

We recently had a paper accepted for publication, called “Modulation of BK Channel by MicroRNA-9 in Neurons After Exposure to HIV and Methamphetamine.” The history of the paper is an example of how research can take unexpected turns. We started out by quantifying microRNAs in the brains of HIV positive patients with and without a history of diagnosed drug abuse. We applied lots of statistics, did some reading, and figured this one (out of possible 384), microRNA-9, might be worth looking into further. It turns out that one of its functions was to inhibit the production of the larger splice variants of the BK Channel. So essentially, this RNA molecule causes the protein shown above have its ends missing — the parts that I highlighted in yellow.

We know that it has some regulatory components in it, the region highlighted in yellow can affect the shape of the BK Channel and it can affect how other proteins interact with it. We don’t know for sure yet exactly how, until someone does more experiments. We showed in our paper that neurons exposed to factors from HIV-infected immune cells and also to methamphetamine have increased amounts of microRNA-9 (how/why? — don’t know yet); and this causes higher proportions of the short form of the BK Channel (missing the yellow regions) in neurons that are susceptible to drug-abuse in the brain (dopamine neurons). We suspect it causes a delay in return to resting potential. This would impact how the brain processes anticipation & reward. I always like to use this tool, called CN3D, to have a look at the proteins or molecules we’re studying. Of course, we have no way to actually see them with our own eyes; but physical protein chemists have a way of determining what their structures are, and we have technology to represent them visually in ways that are meaningful to us. There is a link on the right-hand side of this page to the CN3D page, the software is free, and you can access any protein you’re interested in through the National Center for Biotechnology Information. It’s a really cool project and lots of fun to look at the different renderings and rotate the rendering around in three dimensions. Some of them even show drugs, ions, cofactors interacting with the protein.

To me, it’s interesting to think of the shape, location, and how form relates to function in this way. In the lab, these things are repesented as blobs on a Western blot, or color changing in a solution, or a glowing bar on a gel — looking at these structures is much more inspiring. From left to right, these are the views of the BK Channel that are above.

  1. Secondary structure, showing α-helix and β-sheets — how the protein folds to make a three dimensional object.
  2. Just the peptide backbone — proteins are generally one long molecule, like a polymer, with repeating motifs called a peptide linkage; this view shows the the backbone folds.
  3. Wire view — representing all of the atoms on the molecule; as lines showing the bonds that link them together.
  4. Ball & Stick view — this is the classic structure showing the atoms as balls and bonds that link them as sticks. Sometimes they are colored by element.
  5. Space-fill view — this represents what the structure actually would look like; the size of the spheres are proportional to the size of the atoms, depending on what element it is, and the rending is opaque so we can’t see through it.

The cool thing about this is that you can color-code it as well based on physical properties of the regions of the protein — how greasy it is, how polar it is, with parts of it are positively/negatived charged, or neutral. A few of these views, and rotated to get a side-view are shown below. Imagine the middle region being intersperced with fatty lipids that form the membrane of the neuron; on top is the outside of the cell and on bottom is the inside — its job is to move the K+ ions against a gradient to recharge the potential difference across this microscopically thin membrane.

Other renderings of the BK Channel. The left views are from the side, with the outside of the cell on top & inside on bottom; the middle portion of the protein passes through the fatty lipids that form the cell's membrane. On the left: hydrophobicity -- brown means the parts of the molecule that favor grease/oil and the blue are the parts that favor water; the middle show the positive (red) and negative (blue) charged side-chains. Far right - top-down view of the structure with the ball-stick view of all the atoms.
Other renderings of the BK Channel. The left views are from the side, with the outside of the cell on top & inside on bottom; the middle portion of the protein passes through the fatty lipids that form the cell’s membrane. On the left: hydrophobicity — brown means the parts of the molecule that favor grease/oil and the blue are the parts that favor water; the middle show the positive (red) and negative (blue) charged side-chains. Far right – top-down view of the structure with the ball-stick view of all the atoms.
Advertisements

One thought on “Proteins are Dynamic & Cool

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s