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Proteins
Proteins
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What are they?
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What are some examples of proteins?
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Worker molecules that do jobs in your body
Hemoglobin – in your blood cells for carrying oxygen to your
muscles
Amylase – in your saliva for breaking down your food
Myosin – in your muscles to make them contract
Kinesin – in your cells to help transport big molecules around
What are proteins made of?
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Amino acids
What are these amino acids things?!?
Essential amino acids
Find the amino acid!
 Valine
Hydrophobic
 Small
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 Where
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Inside!
am I?
Find the amino acid!
 Lysine
Positive charge
 Large
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 Where
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am I?
Outside!
Find the amino acid!
 Tryptophan
Hydrophobic
 Large
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 Where
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Inside!
am I?
Protein Folding
Amino acids hooked end-to-end
like beads on a necklace
Twisted and folded into the their final
shape, which allows them to do their jobs
Why do we care about folding anyway?
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Understanding diseases
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We think some diseases are caused by proteins getting messed
up during folding. Can you think up some examples?
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Alzheimer’s disease
Mad cow disease
Parkinson’s disease
Huntington’s disease
Designing proteins to cure diseases
How does folding work?
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Stable is better!
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Don’t let the amino acids bang into each other
Smaller (more compact) is better
Oil doesn’t mix with water
Hydrogen bonds (like magnets) and sulfur-sulfur bonds (like
superglue) help make it stronger
How do we figure out how proteins fold?
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Give a BIG, POWERFUL computer the amino acid
sequence of a protein
Then wait,
and wait,
and wait,
and wait….
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Anton, a special computer designed to solve these
problems, took 100 days to simulate 1 millisecond of
folding
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How long would it take to Anton to simulate 1/10 of a second?
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27 years
Why is this hard?
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VERY,VERY large number of “poses” of protein
 ~10143 poses of single protein
 Only ~1081 atoms in the universe
Proteins fold in << 1 second
Bigger proteins don’t take much longer to fold, but are
much harder to simulate
So…
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Must be rules that let proteins find correct pose quickly
Can’t test every pose, so have to be clever
What is Foldit?
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Computer game developed at by computer scientists at
University of Washington (in Seattle)
Big idea: humans are good at using intuition to solve puzzles
Success!
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Foldit players helped figure out the structure of a protein related to
AIDS, which scientists had been trying to figure out for 15 years!
The structure can now be used to help create new medicines for
AIDS
Foldit players figured out (on their own) state-of-the-art algorithms
Some Foldit players are better than the scientists who made the
game. They were invited to Seattle so that the scientists could learn
their strategies.
All sorts of people play Foldit. Maybe you can help with the
next breakthrough in protein structure!