Protein folding is essential to life. Mad cow disease, or bovine spongiform encephalopathy (BSE), is a fatal brain disorder that occurs in cattle. Abnormal protein folding is considered crucial to the onset of the disease.
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Mad cow disease, or bovine spongiform encephalopathy (BSE), is a fatal brain disorder that occurs in cattle. Abnormal protein folding is considered crucial to the onset of the disease.
To illustrate the concept of protein folding we chose villin, a protein which exists in the stomach and intestine of animals (including homo sapiens).
What causes mad cow?
Try protein folding!
Why do proteins fold?
In a bovine epidemic that struck the UK in 1986, 170,000 cows appeared to be mad: they drooled and staggered, were extremely nervous, or bizarrely aggressive. They all died. As the brains of the dead “mad” cows resembled a sponge, the disease was called bovine spongiform encephalopathy, or BSE.
Other examples of spongiform encephalopathy are scrapie which develops in sheep, Creutzfeld-Jacob Disease (known as CJD) and its variant form (known as vCJD) which develop in humans.
Dr. Prusiner, in 1982, identified the infectious agent responsible for transmitting spongiform encephalopathy in “proteinaceous infectious particles”, which he named prions.
Prions are proteins that are found in the nerve cells of all mammals. Many abnormally-shaped prions are found in the brains of BSE-infected cows and humans afflicted with vCJD or CJD.
The difference in normal and infectious prions may lie in the way they fold.
Humans may be infected by prions in 2 ways: 1 - acquiring the infection through an infecting agent (through diet or as the result of medical procedures such as surgery, injections of growth hormone, corneal transplants, possibly blood transfusion);
and 2 - hereditary transmission.
Brain surface of CJD patient on autopsy
showing sponge-like appearance
How do prions fold?
How do proteins fold?
Evidence indicates that the infectious agent in transmissible spongiform encephalopathy is a protein. Stanley Prusiner pioneered the study of these proteins and received the Nobel Prize in 1997. He has named them prion proteins (referred to as PrP) or simply prions.
Proteins have primary structures, which is their sequence of amino acids, and secondary structures, which is the three dimensional shape that one or more stretches of amino acids take. The most common shapes are the alpha helix and the beta conformation.
The normal protein is called PrPC (for cellular). Its secondary structure is dominated by alpha helices. The abnormal, disease producing protein called PrPSc (for scrapie), has the same primary structure as the normal protein, but its secondary structure is dominated by beta conformations.
The “kiss of death”
A person ingests an abnormally-shaped prion from contaminated food or other contaminated sources.
The abnormally-shaped prion gets absorbed into the bloodstream and crosses into the nervous system.
The abnormal prion touches a normal prion and changes the normal prion\'s shape into an abnormal one, thereby destroying the normal prion\'s original function.
Both abnormal prions then contact and change the shapes of other normal prions in the nerve cell.
The nerve cell tries to get rid of the abnormal prions by clumping them together in small sacs. Because the nerve cells cannot digest the abnormal prions, they accumulate in the sacs
that grow and engorge the nerve cell, which eventually dies.
When the cell dies, the abnormal prions are released to infect other cells.
Large, sponge-like holes are left where many cells die.
Examples of alpha helices
and beta sheets
Like all proteins, villin is formed by a unique sequences of amino-acids. However, only knowing the sequence tells us little about what the protein villin does and how it does it.
In order to carry out their function (for instance as enzymes or antibodies), proteins must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding."
Villin’s function is to give structure to intestinal villi, which are a bundle of actin filaments. Intestinal villi augment the surface of the intestine to increase food absorption. However intestinal villi need to be “stabilized”, to add rigidity. Villin accomplishes this goal by folding in a certain particular way in which it attaches to actin (another protein) filaments at specific receptor point. One and only one way of folding is the correct way.
Distributed dynamics simulate the complexity of the mechanisms of protein folding, which happens extremely rapidly.
Forms determines function
Suppose you have some molten iron. You may turn it into nails, hammers, wrenches, etc. What makes these tools different from each other is their form (i.e. their shape and structure).
Try protein folding!
Proteins fold, amazingly quickly: some as fast as a millionth of a second (microsecond).
While this time is very fast on a person\'s timescale, it\'s remarkably long for computers to simulate.
Dr. Pande at Stanford University applied an innovative computational method and large scale distributed computing (called [email protected]), to simulate timescales thousands to millions of times longer than previously achieved. This has allowed him to
simulate folding for the first time.
Distributed dynamics is like processing something in parallel. It means breaking down a large task into smaller tasks and assigning them simultaneously (i.e. in parallel) to a number of resources instead of assigning them to one resource that can get to each task one at the time. The overall large task will thus be completed faster.
Your local post office provides a good analogy to distributed dynamics. The one at the left has only one window open. The one at the light has three. To which one would you rather go if you are in a hurry?
Results from [email protected] simulations of villin
Since October 1, 2000, almost 1,000,000 CPUs worldwide have participated Dr. Pande’s computational research [email protected]
How can you help?
Everybody can help the project by downloading the necessary software at the link shown at the side and running our client software on their computer.
For every computer that joins the project, there is a proportional increase in simulation speed.
Download the software in your classroom and make your school be part of an exciting cutting edge research that can benefit advancements in medicine and biology.
Using the down time of your computer connected to the web the [email protected] client softwareshows real time visualizations of the protein simulations being performed.
The molecule drawn is the current atomic configuration ("fold") of the protein being simulated on your computer.
For villin to correctly attach to the actin filaments it needs to fold so that it can attach to the receptor sites of the actin filaments. We have simulated this fast naturally occurring process by means of magnets, which are attached to the villin protein and to the actin filaments. While each bend can fold in more than one direction, you will have to find the correct set of folds for the two bend that are show in the model for villin to properly attach.
Go ahead and try. Are you able to find the set of moves that gives you a perfect attachment?
Once you have succeeded, you have simulated what happens in our bodies millions of times every day, in million of possible alternatives.
The model shows how the villin protein might look if you were able to see it at the molecular level and if each amino acid was kind enough to be naturally color coded. Each sphere represents an amino acid, each different color represent each type of amino acids (36 in total).
Villin has been heavily studied experimentally and by simulation since it is perhaps one of the smallest, fastest folding proteins.
It has a hydrophobic (i.e. water hating) core made of two groups (phenylalanine - blue and anotheralanine - gray), but also has two groups (a tryptophan – light orange and another lysine - green) which are hydrophilic (i.e. water loving).
Are you a high school teacher of Chemistry or Biology? Are you interested in teaching protein folding? A set of ready-to-use classroom resources, aligned with California Science Standards, can be downloaded from the web.
General description of project components
It is linked to the “Snack Presentation”, described below.
linked to a lesson plan that asks students to compute the molar mass of Villin.
hydrogen bonding, using wood dowels and magnets.
To Fold or
Not to Fold?
The Biology of
Photo of Snack
Michael Crichton, Prey, Harper Collins, 2002
How the cows turned mad, Maxime Schwartz, University of California Press, 2003
Jeremy Cherfas, The human genome, Dorling Kindersely, 2002
Mark Ratner & Daniel Ratner, Nanotechnology, Prentice Hall