Wednesday, March 9, 2011

How to fold a Protein - and how to do it wrong.

Since it's been a while since my last scientific blog post, I thought I could seize the opportunity and use my presentation theme for Miolecular Biology. The presentation is going to be on Thursday and my group will talk about Protein Folding & Prion Diseases.

If this sounds too complicated to you - don't worry. I'm only gonna explain the basics (because I don't know any better either XD) BUT it will be in English. Maybe I'll add a translation at the end of the post, but basically everyone who understands English should be also able to understand this topic :) (since my study programme is wholly in English it's easier for me to talk about these things in English, furthermore I see it as a good opportunity to practice my English)

I (kind of ignored my group and) chose Prions as a topic for the presentation because Prions fascinate me since I learned about them around the beginning of the new millenium. Back then there were first cases of BSE in Austria, a disease which I had never before heard about but which scared the hell out of everyone. Restaurants in Austria even refused to serve beef, and people were panicking about the disease, but nobody really new what it was, so I started to research a bit on the topic. Back then I was 10 years old and had no idea about protein chemistry or protein synthesis.
Today I understand more about proteins, but this only helped me to understand that up until today, Prion diseases such as BSE or Creutzfeld-Jacob-Disease are not more than rudimentarily understood and researched.

First I'd like to give you a basic introduction in Protein synthesis and Protein Folding. Don't worry, it won't get too complicated and you probably heard about most of it in school.

Basically, the DNA in each of our cell's nuclei codes for the proteins. Proteins, again, make up almost everything in our body. As an example, there are specific proteins in a cell's membrane, that work as ion channels and it's their job to maintain the ion concentration inside the cell at a certain level. Other proteins work as enzymes - catalyzing agents that make vital, chemical reactions in our body work. And there are many, many more.

So how is a protein synthesized?
The DNA-code in the nucleus is copied into an RNA strand, this process is the infamous Transcription.
A so-called ribosome attaches to the RNA strand and starts to "read" out the original code. According to that code the ribosome assembles single amino acids (the building blocks of a protein) to a polypeptide chain (one amino acid = peptide ; a chain consisting many amino acids = polypeptide) during the so called Translation.

The picture shows the process of protein synthesis in more detail.
(picture source:*klicku*)

So far most people will probably recognize this from school.
But for a fully functional protein, this polypeptide chain needs a very specific, three-dimensional structure.
This structure mostly depends on the amino acids that make up the polypeptide chains.

A single amino acid consist of an central Carbon-Atom (called α-Carbon Atom), with an amino group (NH3+), one H-atom and a carboxyl-end (COO-). The fourth binding partner (rember: C always forms 4 bonds! Always, always, always. Helps a lot when drawing molecules in oragnic chemistry.) is called the side chain, and each of the 20 amino acids has a different side chain with different chemical properties (hydrophobic/hydrophilic; acidic/basic, Hydroxyl- or Sulfur-containing).
The single H-atoms that are attached to the backbone may interact with electronegative atoms of other amino acids (e.g. oxygen atoms). This determines the so-called secondary structure. The polypeptide chains form loops or flat structures, the most common secondary structures are the α-helix and the β-sheet.
But the side chains can interact with each other as well. Due to their different chemical properties they arrange in a ceratin structure towards each other, e.g. usually the hydrophobic parts usually assemble in the central part of a protein. The side chains can also form so called salt bridges (weak connections of ionic ends of the side chains), H-bonds and covalent bonds. Alltogether these interactions determine the tertiary structure of the protein (the arrangement of the helices and sheets towards each other).
Since there are often many different ways the side chains could interact (especially in longer polypeptide chains) they often require so called chaperone proteins ("helper proteins") that assist the chains in attaining their right conformation.

Klick on the Picture if it is not displayed properly!

The picture shows the protein Ribonuclease A. Of ist 124 amino acids, it contains  8 sulfur containing sites that may connect to disulfide bridges. On the left you see the denaturated version of protein, where the intramolecular forces do not act (this may happen due to increase in temperature or certain chemicals). If the protein renaturates, it may happen that the wrong disulfide bridges are built (in the middle). Only if the right environmental circumstances are given the right conformation will assemble.
picture via *klicku*

Now that we've talked about the process of protein folding, it quickly comes clear that this is a very complex process. And the more complex a process is, the more can go wrong.
Just imagine a slight mutation in the DNA, that suddenly causes the coding of a different amino acid than before. This new AA may have a side chain that acts completely different from the original (hydrophilic instead of hydrophobic, for eyample), therefore the structure is disturbed.
But this is not the worst case scenario. Even if such a mutation occurs in one cell, the cell will sooner or later die and a new one will replace it.

But the misfolding of a protein can take "going wrong" to a whole new level, when the protein suddenly starts to force other proteins to fold into the wrong, pathologic conformation too. Such proteins are also referred to as "rogue proteins", and they can cause a fatal, biochemical chain reaction in the body.

A good (or should I say bad?) example for such a protein is the Prion protein.
It can be found in nerve tissue, and actually nobody knows what it really does. But this shouldn't bother us, since it doesn't harm us either.
Unless it obtains the wrong conformation.

Prion Protein (left: normal configuration, right: misfolded version) via *klicku*

On the left side of the picture you see a normal prion protein. It has a characteristic α-helix structure, which is in the abnormal prion protein reassambled as a β-sheet.
This has two consequences: Firstly, the prion protein becomes a rogue protein, which, as I mentioned above, can turn other porteins into this new conformation.
Secondly, this new protein structure has the very unpleasant characteristic to make the proteins cluster in so called amyloid plaques. They accumulate in the nerve tissue and cause deterioration of the brain, as the nerve cells and their connections wither.

These protein-plaques in nerve tissue are associated to various so called spongiform encephalopathys. These are diseases where the brain is slowly "dissolved". It literally turns into a perforated, spongy mass (hence the name).And here we get to the most interesting but also most disturbing part.
From here on, you will probably find contradicting information on almost everything I can tell you. The problem with prion diseases is, that the modus operandi, the way how they "work", is not completely understood.
Just take Alzheimer's disease as an example. Up until now, it is not fully understood what exactly happens to the brain during that disease. But it has been, in some theories, associated with amyloid plaques like the ones formed by prions. It is therefore sometimes assumed that Alzheimer's disease is a consequence of protein misfolding.
Other diseases associated with protein misfolding and accumulation of amyloid plaqes are Huntington's disease and Parkinson's disease.

So let's go back to the prion caused diseases about which I can tell you a bit more (even though all my information is just taken form books and websites, I hope at least half of it is more or less true and state-of-the-art).

You probably remember the cases of BSE and the panic that was caused by them.
BSE means bovine spongiform encephalopathy (often also referred to as "Mad Cow Disease" or MCD, because of the aggressive behaviour the affected cows show towards humans) and it is a disease caused by prions.
During the second half of the last century, it was very common to feed bone meal (which basically consits of grinded leftovers from slaughtering) to cattle als a protein supplement.It was used as a cheap alternative to the more expensice "vegetarian" protein supplement which is ususally soy beans.
 In 1986 the first animal fell ill to the beforehand completely unknown BSE in the UK. It is nowadays supposed that insufficiently sterilized bone meal caused a transmission of infectious prion proteins to cattle. Usually the bone meal has to be heated before it gets fed to the animals but in the UK these restrictions were lower than in other countries, which may explain why the disease broke out there first. There are also some theories that suggest that the scrapie prion (scrapie is a form of spongiform encephalopathy in sheep and goats) contaminated the bone meal.
So anyway, there were more and more cases of BSE in the UK, and many animals had to preventively slaughtered and burned to avoid further spread of the disease. However, over the time a new disease developed in humans, which, in retrospective, was probably caused by the consumption of contaminated beef.
This new disease in humans was called variant Creutzfeld-Jacob-Disease or vCJD due to its striking resemblance to the Creutzfeld-Jacob-Disease that was for a long time known in elderly people. But the new, vCJD also occured in young people (around 30 years).
This shows that prion-diseases are not specific to a certain host - transmission between different species is possible. The actual nature of a prion would explain this quite well - since it is an infectious agent that is nothing like a bacterium or virus, without any genetic material, it may be hazardous to any host as long as there are other proteins in this host that can be changed to their wrong conformation.

The crazy thing about this is that there also seems to be some genetic influence on how these diseases develop.
Certain genes were associated with prion diseases such as CJD in humans but also scrapie in sheep. However, there were secluded groups of sheep found in New Zealand, which had the mutation for scrapie (which basically means that they were 100% likely to express the faulty protein) BUT they did not show any symptoms of the disease!
So this means that they had to mutation for scrapie, but had no scrapie.Therefore it is believed right now, that the method of spread of prion diseases (at least scrapie) is a combination of a genetic "likeliness" to fall ill with disease, and coming in contact with an infectious agent, like it happend at some point to the humans who ate contaminated beef.

Talking about contaminated beef: Nowadays an infection with vCJD due to contact with contaminated beef has become less likely, since more attention is paid on the accuaret removal of any nerve tissue from meat while slaughtering. Nevertheless, eating intestines, and those parts of meat that may contains bits of the spinal cord or brain tissue, is more risky (this includes sausages such as hotdogs.).

However, a vegetarian diet does not necessarily mean it is impossible to get CJD. You may only actively avoid getting vCJD, but there are other types of CJD, such as the inherited and the sporadic/classical CJD (sometimes in literature they are not distinguished, so it is hard to tell which of the information about this topic is really relevant).
Inherited CJD is caused due to a genetic defect, which causes the expression of faulty prion proteins. There are various genetic defect that may cause the expression of a faulty prion gene, and they are all dominant. The symptoms usually appear before the age of 55 and develop over a period of up to some years.
In comparison, the sporadic or classical CJD, is not related to an inherited gene, it is rather believed to be naturally occuring condition. This means that it is not caught from another person or animal, not passed on from your parents or to your children and does not depend on your diet. It can appear in everyone, even vegetarians. From what I've read so far, I suppose that is probably related to old age, since the disease shows at an age of 55 to 75. This is the most common type of CJD and there is approx. 1 case per million people.

Symptoms of the disease vary slightly depending on the type of CJD, but generally the early smyptoms are changes in personality, deperession and loss of interest in life. While these symptoms worsen over time, new ones will appear, such as confusion and memory loss for the people with sporadic CJD, whereas in vCJD patients, the depression gets worse and anxiety, delusions and hallucinations are common.
Other symptoms inlcude: loss of balance, general problems with movement, problems with seeing and hearing, memory and speech loss, muscle paralysis and incontinence. Eventually, people go into a coma and die of infections.

So far, both versions of CJD are incurable and always end fatal. The only medication available may slow don the deterioration of the brain, but there is no such thing as a cure.

As sad as this fact is, for me it is an incentive.
Prion diseases show us humans, that we may be able to decode DNA and perform genetic engineering, but there are still many things that we do not understand at all, even if they appear simple at first. The deeper you go into that topic, the more confusing and contradicting information you will find.
Maybe, one day, we will be able to understand such diseases and even cure them. And I really hope that I will one day be able to contribute to all the research that is going in on in order to find out more about incurable diseases.

I hope I was able to give you an (more or less) interesting insight in this topic, if you're left with any questions, don't hesitate to ask them. Also, if you have any suggestions on further (scientific, but also everything else) topics that you would like to hear about - I'm happy about any input that I can get :)

German version available, if you would like to read one.

Sources of Information:
Bettelheim et al: Introduction to General, Organic and Biochemistry; 2010 Brooks/Cole; Canada
Greenwood et al: Medical Microbiology, A guide to microbial Infections; 2007 Elsevier Ltd.


  1. *Varis used 1000-Science-Facts*
    *It was super effective*
    *Blorg fell asleep*

    _ _ZzZZzzZz

    also 50% hab ich schon geschafft,
    die andere hälfte les ich später ^^'
    gut das ich sowas nicht auswendig
    lernen muss, auch wenn's gaaanz einfach ist :p

    grüssli ^~

  2. mmerhin hast du die hälfte gelesen, was doppelt so viel ist wie ich ursprünglich auch nur von irgendwem (der sich nicht schon vom titel hat abschrecken lassen) erwartet hätte XD

  3. du magst mich doch echt töten oder :D
    mal sehen wann ich das alles lesen kann xD

  4. Ach, du musst es doch nicht lesen XDD Ich dachte mir schon dass es wahrscheinlich nur sehr wenige interessieren wurde ;)

  5. mich interessiert es aber :D
    deswegen aber so lange Texte machen mir momentan Kopfweh xD

  6. Ich habs komplett gelesen! XD
    Und ich fand es sehr interessant :-) Im Bio-LK im Abi haben wir zum Teil auch einiges in die Richtung gemacht und ich fand es da schon super spannend. Ich finde es immer wieder so beeindruckend und faszinierend, wie komplex die Vorgänge in unserem Körper sind!
    Dein Englisch ist wirklich gut zu lesen und du hast das Thema sehr verständlich erklärt... also danke für den Post! ^__^


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