The protein folding revolution

The protein folding revolution


Proteins carry out the labor in our cells
— so we really need to know what they do and how they work. The key to proteins is their shape because
that dictates their function. They can take many different shapes. Scientists call these folds. Unfolded, a protein is a long string of amino acids. There are 20 different amino acids and each
one of them has its own chemical behaviours. When a protein folds up, you get a long tangled
piece of spaghetti with all these different chemical functionalities on it It’s not exactly like spaghetti – because
its 3D shape evolved over billions of years to do very specific jobs.
If you can understand the minute details of the structure of proteins– not only do you
get insights into their function — you might be able to change that function. So researchers have been trying for many years
to solve the protein folding problem: Can we just look at the sequence of amino acids
and predict how a protein is going to fold? You could take the amino acid sequence, plug
it into a computer, and see if your algorithms are good enough to make sense of how it might fold. You can use X-ray crystallography or
other techniques to image a protein structure but that hasn’t been done for very many kinds of proteins. A couple of decades ago folks asked a separate
question –could all the genome sequence data- the three billion letters in our genome and
the billions in all the other genomes out there – could they scan that code, which is
separate from the amino-acid code of proteins, and learn anything about how proteins might fold? The DNA in our genes codes for RNA, which
is translated into proteins. So there’s a relationship between the 4-letter DNA code
and the 20- letter amino acid sequences of proteins. Because a protein wraps around in many different
twists and turns–the 6th amino acid in that chain might end up next to the 18th amino acid. If they end up next to each other, researchers
realized there might be an interaction between the pair that is critical to the shape of
the protein and therefore its function. If that’s true then a mutation in the DNA
that changes one of the amino acids must be accompanied by another mutation to the other
member of the pair to preserve the interaction. In essence, they co-evolve. Well, if you can log maybe a hundred or more
of those cases of close-by neighbors in 3D space, based on looking at many genome sequences, then you plug that into your folding program.
Now that it has all these tight constraints it gives a much better chance of getting a
really accurate structure. And it works! The upshot is scientists can fold lots of
proteins that they never could before. That’s important because it will give new
insights into how those proteins work. Beyond that-researchers have been steadily
improving the ability of computers to model the shape of proteins, and this now enables
them to design their own proteins—making things never seen before in nature. The most obvious application is medicine. They can target very specific parts of the
flu virus with a special built protein– enabling a vaccine that works across flu strains They’ve designed proteins that naturally assemble
into tiny cages that can deliver different molecules in the body Or, new materials,like engineered surfaces
that self assemble could be used in solar cells and electronic devices. you can go in a thousand different directions.

27 Replies to “The protein folding revolution”

  1. Superb video, proving the need of interdisciplinary approach to understanding evolution's awesome solutions. I love the way the video was made interwining the beauty of the art, especially in the ending!

  2. I think there might be a typo in the text the commentator is reading.
    Minute 1:34 to 1:38
    "So, there is a relationship between the FOUR letter DNA code and the 20 letter …"
    Unless there is new proof that the DNA code consists of four letters, not three.

  3. The massive amount of computing power required to run these types of predictive queries is astounding.

    Any lay person can help though by running software on their computer in the background that donates your spare CPU cycles to running these experiments. A couple great projects that allow the public to get involved like this are:

    [email protected] out of the University of Washington: –> http://boinc.bakerlab.org/rosetta/
    and
    [email protected] out of Stanford University –> http://folding.stanford.edu/

  4. Protein evolution is impossible. Unintelligent, unguided forces of nature could never form functional proteins.

  5. You can help these scientists to better understand how folding works and maybe find a cure for diseases such as cancer, Alzheimer… using your computer's CPU power
    http://folding.stanford.edu/

  6. copy what nature already created is one thing, but create new proteins is a NP complete problem, you would need a computer the size of the Sun to do it

  7. The lady narrating this sounds like Sarah Koenig from the Serial Podcast. She did it really well too, easily understood! Thanks!

  8. Current peer reviewed research shows by the numbers new protines cannot and did not evolve. Protine research has not produced or predicted a single new fold…ever.
    This video is very deceptive, but cool graphics!

  9. This entire video seemed like an introduction. I am supposed to take notes on it and I was waiting for the introduction to pass to start taking notes but it ended.

  10. Why study all of these complex molecules and their function while at the same time destroying all if it before ingesting it into our bodies when we eat?
    A billion years of evolution says it must serve some purpose.

  11. Really bad science to say 'evolve'. The probability of 150 aa chain (small protein) has a probability of coming together as 1 x 10 to the 164 power. Far less likely hood of finding a specific atom among all atoms in the observable universe. Good video otherwise. My vote for something this amazing is Intelligent Designed, not the Darwinian fairy tail described.

  12. I find this really interesting! When I'm done studying chemistry this is the area of science I want to do research in.

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