CHEM 106

When I watched the videos on the syllabus for this week, I was surprised to learn that yeast was so important in the discovery of mutated prion proteins. I had not really heard of the importance of yeast in scientific experiments before, but after some investigating I discovered the many benefits of yeast to scientific research. As stated in the video, yeast cells are very similar to human cells. Like human cells, yeast cells have eukaryotic structure. This means that its cells contain a nucleus and other organelles enclosed within membranes. Yeast has about 6,000 genes, while the human genome has about 25,000. Yeast and human cells do share many genes though, so if you wanted to test how a certain human gene responds to something, you can often test yeast cells first. One of the greatest characteristics of yeast cells that make them perfect for scientific experimentation is how quickly they grow. Human cells divide a rate of about once every twelve hours, yeast divides about once every two hours. Therefore, scientists can complete experiments much faster with yeast cells than with human cells.
Yeast has been used in many other experiments besides the research on prion proteins. NASA has sent a satellite into orbit carrying a laboratory full of yeast to tests whether certain organisms are more resistant to drugs in outer space. Outside of the scientific field, yeast will always have a place in my heart and at my table as both bread and beer.

Prion Disease

After learning about a little bit about proteins and DNA in class last week, I found an article about how researchers are finding new ways to improve vaccinations. Instead of inserting a weaker live or dead virus into a person to create immunity, scientists want to use DNA vaccines, which would use the DNA to produce proteins against the virus, resulting in faster immunity.

It disproves common ideology that cells shut down when foreign DNA is introduced. With the right type of DNA, cells can react very differently than expected. This would also improve other treatments like gene therapy for Parkinson’s, hemophilia, leukemia, and other serious illnesses. This kind of therapy could improve specific protein production in a variety of cells, leading to further research and cures.

http://www.utexas.edu/news/2015/03/05/protein-boostergene-therapy/

In the prion diseases video, Susan Lindquist explained the importance of protein in our bodies. So I looked up proteopathies, diseases that are caused from the malformation of proteins in the bodies. Prion diseases are a type of proteopathy.

One thing that stood out to me about proteopathy is their often very different symptoms.

A lot of protein problem diseases have neurological symptoms: Alzheimer’s disease, Parkinson’s disease. But others do not:  type 2 diabetes, amyloidosis.

In this post, I will look at the role of proteins in type 2 diabetes.

Type II diabetes is the most common type of diabetes (making up 90% of cases). Since 1985, the cases of type II types have risen from 30 million people to 285 million, mostly attributed to the rise of obesity. It is a metabolic disorder that results in high blood sugar because of a lack of insulin. The symptoms of type II diabetes are excess thirst, frequent urination, and constant hunger.

Type II diabetes is caused because beta cells do not produce enough insulin. This means that cells in the liver produce glucose when they do not need to.

Another relation between Type II diabetes and protein is that some doctors recommend patients eat more protein than people with diabetes.

Prion protein diseases as neurodegenerative diseases along with the video on the impact of prion proteins on brain cells, got me thinking about how these mutated protein structures have the ability to affect certain functions controlled by our brain and how this process occurs.
Prion proteins so potently affect our brain function because the normally occurring prion protein is found in our brain cell membrane. However, the deformed structure of this protein is poisonous for brain cells. I read an interesting article on research conducted by Adriano Aguzzi, that describes the entire process as being controlled by a ‘switch’ that the prion protein has, which controls its toxicity. This switch covers a small area on the protein’s surface and if another molecules comes into contact with this switch, it immediately triggers cell death.
Prion protein molecules consist of two functionally distinct parts: a globular domain, which is tethered to the cell membrane, and a long, unstructured tail. This tail is vital to the prion protein because it dictates the functioning of our nerve cells. However, in an infected prion protein, this tail serves the opposite purpose as it comes into interaction with the globular part, triggering the ‘switch’ and leading to cell death.
Therefore, this has led to a groundbreaking conclusion for prion disease cures. It stresses the importance of the prion tail in these diseases as it causes cell death. It also suggests that prion proteins with a trimmed version of the flexible tail cannot damage brain cells, even if their switch has been recognized by antibodies. If the tail is bound and inaccessible using a further antibody, activation of the switch can no longer trigger cell death. These findings reveal that only antibodies that target the prion protein tail are suitable for use as potential drugs. By contrast, antibodies that trip the switch of the prion are very harmful and dangerous.

This week in class we learned about alpha helices and beta sheets in protein structures. It’s thought that prion proteins become infectious when some of their alpha helices are converted into beta forms. I did a little research to find more details on the structure of the normal and infectious structures of the prion protein, and found something interesting: Not only is the conversion mechanism between the two forms unknown, but the structure of the infectious protein itself is unknown as well.

There have been recent, ongoing efforts to determine the structure of this protein (PrPSc), so I tried to find information that would be up-to-date. A paper from February, 2014 gave a good review of multiple attempts at modeling PrPSc, including both the methods of determining the model and the proposed structures. The methods of determining the structure included techniques such as Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance spectroscopy (NMR), and X-ray crystallography.

One interesting fact that I learned is that old analyses of PrPSc thought that alpha-helices made up some portion of the protein because of FTIR data. There was a specific peak on the spectra that had been attributed to alpha helices, but it turned out later on that this peak showed up even when no alpha helices were present. Therefore, we cannot be sure whether PrPSc contains any alpha helices or not.

Another interesting fact that I learned is that many scientists who model PrPSc seem to think that there might be a beta helix present in the molecule rather than a beta sheet like the ones we learned about in class. A beta helix is a spiral of multiple beta strands (the straight, individual strands of amino acids that make up beta sheets). This structure would be stabilized by the same kinds of hydrogen bonds that we learned about. A beta helix might look something like the image below, where each arrow is an individual beta strand:

Overall, it’s cool to think about all the secondary structures that might be present in proteins, and how scientists try to go about determining which of those structures a molecule has.

I found the models that we were able to construct in class on Thursday to be very interesting! It was fascinating to see how the hydrogen bonds and different geometric bonds of the elements could affect the shapes of the amino acids so drastically!

I returned back to my research on prions from last week and was fascinated to see that a traditional PrP (prion protein found in mammals) is constructed of three α-helices and a two-strand antiparallel β-sheet, an NH₂-terminal tail, and a short COOH-terminal tail.  Before having constructed those models in class, I would have had no idea what an alpha-helix or beta-sheet was! Additionally, it is interesting to note that a traditional PrP is 208 amino acids long and has two distinct isoforms: PrPC which is a healthy major prion protein, and PrPSc (the Sc stands for scrapie) which is the infectious structure of a major prion protein.

I have included a picture of the structure in the link of a PrP so that you can see the alpha helices (in green) and beta sheets (in blue) and how they are altered when a PrPC is infected and becomes PrPSc!

http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2005/Winter/Prion1new1.htm

Prion diseases are rare progressive neurodegenerative disorders. Prion diseases tend to progress rapidly and to be fatal; characteristics include brain damage, long incubation periods, and lack of inflammatory response. Prion diseases are distinct because they aren’t triggered by bacteria or viruses, rather they are triggered by infectious proteins. The diseases are caused by prions, abnormally shaped proteins. When PrP- a normal brain protein- twists into an unnatural shape, it remakes other PrP proteins into the same unnatural shape. These prions then clump together into dangerous plaques.

Interested in the “exclusivity” of prion diseases, I decided to find out what type of animals can contract prion diseases of other animals. I came upon an article published in April 2014 in ScienceNews. This article focuses on bank vole PrP’s and the bank vole’s high susceptibility to prion diseases. https://www.sciencenews.org/article/bank-voles-provide-clue-prion-disease-susceptibility

Considering the fact that prion diseases hardly ever transfer from species to species, bank voles, a small rodent similar to mice, are an interesting species to study. Bank voles are unique in that they are especially susceptible to prion diseases. While usually a prion from one species is unable to corrupt PrP proteins of another species, the PrP proteins of bank voles are susceptible to every single prion disease when the prions are directly injected into the brain. Interestingly though, a wild bank vole has never been found to have a prion disease that was developed outside of the lab.

Joel Watts, University of Toronto neuroscientist, and his colleagues studied the PrP proteins of bank voles in order to find out if the vole’s high level of susceptibility was due to the vole’s physiology or to the vole’s PrP protein itself. Watts placed bank vole PrP proteins into mice and then injected infectious prions- ones that mice are usually not susceptible to- into the brains of the mice. While mouse PrP proteins and bank vole PrP proteins are different, they only differ by eight amino acids. The result was that the mice that quickly developed the neurological diseases were the same mice that had large amounts of vole PrP proteins. Thus, it can be assumed from the study that the vole PrP is a “universal acceptor”. This knowledge can be very useful for studying new diseases. Scientists can test if the diseases are prion diseases by placing infected brain matter into the brains of mice carrying vole PrP proteins and then seeing if the mice become infected with the disease. If the mice become infected, the disease is most likely a prion disease.

Having missed the end of our experiment this past week, I was intrigued by the scientific study process in which they conduct observations and study the results to determine the causes of disease outbreaks. As we understood, there is a great difference between genetic and environmental causes of diseases.

In my research, I came across the fact that scientific research is now being conducted on how these two factors interact together, rather than separately. As complex diseases such as Alzheimer’s and Parkinson’s are researched further, without the traditional genetic transfers, yet a genetic trend, this lurking variable of environment gives an added factor that just may be necessary in ‘solving the case.’

This justification makes sense to be less focused research because as long as the disease is being identified with many factors, it can also be cured with fewer of the ‘symptoms,’ meaning just a genetic or just an environmental trigger.

http://www.nature.com/scitable/topicpage/complex-diseases-research-and-applications-748

After learning about kuru in class, I wanted to know more about other kinds of prion diseases, including fatal insomnia. People with fatal insomnia die because, as the disease’s name suggests, they are unable to sleep. I wondered why this symptom is not characteristic of kuru. The answer is simple–kuru damages the cerebellum, while fatal insomnia damages the thalamus, which regulates sleep.

I was also interested to learn that fatal insomnia can be inherited, in which case it is called fatal familial insomnia. If one parent has a specific mutation in the gene for cellular prion proteins (PrP^C), then their child has a 50/50 chance of inheriting that mutated gene and the disease it causes.

In other prion news, just today there was a discussion on NPR about the possibility that research on mad cow disease could lead to better treatment for Alzheimer’s and Parkinson’s. Researchers are considering ways to stop the chain reaction of improper protein folding caused by prions. A recent experiment has shown that neurons can be protected from the damaging effects of a certain kind of misfolded protein by replenishing the neurons’ supply of nicotinamide adenine dinucleotide (NAD). It’s possible that this discovery could help scientists develop treatments that could slow the progress of neurodegenerative diseases.