Wednesday, April 12, 2017


MscL should be protein of the year for many reasons. For one, it is structurally beautiful. It has many protein chains that come together to make one beautiful mechanosensitive channel protein. This protein is essential for bacteria to be able to move into new environments safely. In the pictures below you can see the channel through the protein, as well as the helices that cross the membrane.



 Picture above is colored by structure
 Picture to the right is colored by chain
The picture above is colored by element with side chains hidden.










The picture below is looking down the channel with the side chains shown.. The picture to the right is colored by chain with the side chains hidden.



Imagine a beautiful bacterial cell just floating around in a new solution. If this new solution has less solute than the cell, water would rush into the cell causing it to burst. This would often be a reality, if it weren't for this protein. Its essentially an emergency pressure release valve, but it is mechanically operated. Meaning it opens and closes because of a mechanical stimulus, in this case its pressure. 

There are many mechanoreceptors but not many that we really understand. This protein has helped us learn more about other mechanoreceptors, even though we still don't fully understand how it operates. Looking at the structure in the pictures you can imagine this being inside a cell membrane, and rotating to open and widen the pore seen in the middle. This will allow whatever necessary to rush out of the cell (water, particles, ions, etc.)  in a last ditch effort to keep it from bursting. It has to do this at a very specific pressure, because this is an "emergency" relief valve and doesn't want to be utilized unless absolutely necessary. But, it does want to open before the cell bursts. This protein has the potential to "save the life" of a bacterial cell as it moves into a new environment.

One other beautiful thing about this protein is the fact that we have manufactured things just like this on the large scale. We have made pressure relief valves that function similar to this, that we use in everyday life. They are very effective and can be beneficial to us. I think it's fascinating that something we think we invented was actually functioning in bacterial cells all along. It seems God always has something up his sleeve.

Some of the beauty in this protein lies in the mystery behind it. It is so complicated, that we have yet to figure out exactly how it works, yet we have figured out what it does and it's a fairly simple mechanical task. This protein has helped us learn about mechanoreceptors as a protein class. It's a beautifully simple design that is giving us some more insight into the cell world and how they function.


All of the figures in this blog were made by me using PyMOL using the code 4Y7J.

The information was found from the following primary literature articles:

http://www.ks.uiuc.edu/Publications/Papers/PDF/GULL2001/GULL2001.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4553819/
http://www.nature.com/articles/ncomms11984?WT.ec_id=NCOMMS-20160629&spMailingID=51717127&spUserID=ODkwMTM2NjQyNgS2&spJobID=944164561&spReportId=OTQ0MTY0NTYxS0

Thursday, March 16, 2017

MscL

http://www.nature.com/articles/ncomms11984?WT.ec_id=NCOMMS-20160629&spMailingID=51717127&spUserID=ODkwMTM2NjQyNgS2&spJobID=944164561&spReportId=OTQ0MTY0NTYxS0

This protein is a trans-membrain protein, and a mechanoreceptor.  Mechanoreceptors take mechanical stimulus like pressure, and uses that as a signal for the cell. Most proteins bind to a ligand or something of that sort but mechanoreceptors respond to physical changes in the environment. This specific mechanoreceptor helps the cell not burst during osmotic stresses. It is connected to the bi-lipid membrane of a cell and feels the membrane stretch. It is a homopentamer, and each monomer has two alpha helices that run along the width of the cell membrane. When the membrane stretches, it pulls on the helices and opens the channel. This opens an amphipathic channel that is non selective to about 3 nanometers wide.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4553819/

The MscL protein is the equivalent of an emergency pressure relief valve. In some situations, when the cell is in osmotic shock and unable to compensate, it can burst. This valve allows various different  molecules to rush out of the cell in an attempt to "save its life". It does this by tilting the two alpha helices and opening the channel. The pressure required to open the channel is just before the pressure threshold that would burst the cell. This protein was discovered in 1994, fairly early compared to the other mechano-sensitive channels. Because of this it has been used as a model for understanding other mechanics-sensitive proteins.

http://www.ks.uiuc.edu/Publications/Papers/PDF/GULL2001/GULL2001.pdf

In this article they did a study and discovered that as the channel opened, the helices flattened to open the pore wider, similar to the hinge mentioned in the previous article. They substituted to Gly22 with all the other amino acids and found that the pressure at which the channel opened varied in correlation to how hydrophobic the replaced amino acid was, and the growth inhibition from acidic amino acids. From this and a few other tests they determined that how hydrophobic the amino acids are, and the interactions between the side chains affect how well the channel can shift to open and close.



Wednesday, March 1, 2017




TolC


This is a picture of TolC with the secondary structures shown with alpha helix's and beta sheets. They are differentiated by color.



This is a shot looking down the barrel of the protein, with the side chains hidden. The chains are differentiated by color. 


Another side view, but this time differentiated by chain, and again the side chains are hidden. 


A view down the barrel from the opposite end. This is the side that had the beta sheets. The side chains are colored blue to differentiate them from the rest of the structure. 


This shot is a "mesh" view showing the surface texture. The individual atoms are colored to match. Carbon is green, nitrogen is blue, oxygen is red, and sulfate is orange.