Slashdot Mirror
Proteins Made To Order
ananyo writes "Proteins are an enormous molecular achievement: chains of amino acids that fold spontaneously into a precise conformation, time after time, optimized by evolution for their particular function. Yet given the exponential number of contortions possible for any chain of amino acids, dictating a sequence that will fold into a predictable structure has been a daunting task. Now researchers report that they can do just that. By following a set of rules described in a paper published in Nature (abstract), a husband and wife team from David Baker's laboratory at the University of Washington in Seattle has designed five proteins from scratch that fold reliably into predicted conformations. The work could eventually allow scientists to custom design proteins with specific functions."
Can't you already order proteins at McDonalds?
I want them to synthesize a fully functioning Marylin Monroe to go with my 3D printed vintage sports car.
Do it yourself, because no one else will do it yourself. [beta blockade 10-17 Feb]
32:32 Therefore the children of Israel eat not of the sinew which
shrank, which is upon the hollow of the thigh, unto this day: because
he touched the hollow of Jacob's thigh in the sinew that shrank.
33:1 And Jacob lifted up his eyes, and looked, and, behold, Esau came,
and with him four hundred men. And he divided the children unto Leah,
and unto Rachel, and unto the two handmaids.
33:2 And he put the handmaids and their children foremost, and Leah
and her children after, and Rachel and Joseph hindermost.
33:3 And he passed over before them, and bowed himself to the ground
seven times, until he came near to his brother.
33:4 And Esau ran to meet him, and embraced him, and fell on his neck,
and kissed him: and they wept.
Our efforts to understand how matter becomes life! We will understand it, and we will be able to extend life as a result.
Barring certain genetic anomalies, it should be pretty easy for any husband and wife team to produce protein sequences that result in predicted conformations.
FTFA: "The work was spearheaded by husband-and-wife team Nobuyasu Koga and Rie Tatsumi-Koga"
A centuries-old tradition of origami!
Set your phasers on "funky"!
And it is so well personified in this Slashdot story of how these "enormous molecular achievements" which can have an "exponential number of contortions" evolved themselves into the building blocks all organic life forms. Now we're invited to celebrate the achievement/intelligence of these ones who managed to fold a simple protein that would have folded itself into something far complex and useful, given enough time to "evolve"? Am I the only one who sees the vanity in this reasoning? Why is it so amazing when the intelligence of man achieves something which for those who believe in evolution, is so insignificant in the grand scheme of things? How about we stay quiet until we can create a living thing from scratch that's more impressive than the life-forms the random unintelligent process of evolution has come up with. And if/when you do, know that you would have most likely just reproduced all that you learned from existing life on earth and that would be cheating.
Next step: understand how specific conformations perform their magic in accelerating chemical reactions by factors of trillions so we can design custom enymes.
This is actually a fairly important discovery. The poster of the article seems to be completely clueless as to why it is important.
Without going into all of the details, being able to predict the shape of proteins is one of the things needed to make nanotechnology fulfill its potential - to build a nanotech "assembler".
If you want all the details you would have to go back to "Engines of Creation" by Eric Drexler.
Proteins of the right shape can be used to create complex structures - anything from a virus to a nano-computer. Construct some RNA, feed it into a cell and get back as many copies of the protein chain as you please.
Do this for several different proteins.
Leave all of these proteins in the same chemical soup and they will combine on their own to form the more complex structuresl
But if you can't predict the shape the protein folds into, you can't get started. This has been a key problem in nano-tech going back to the 1970s.
When you are dancing with wolves, never limp
I've always said that protein engineering will become more important to humanity than the transistor, For just one example of the incredible potential proteins have, look at enzymes. These are biological catalysts that tirelessly perform very specific chemical reactions. In the case of some enzymes, they are called 'kinetically perfect', meaning that they are so fast the only way we have of explaining the reaction speed is that every time the molecule they work on collides with the enzyme, the reaction immediately happens. Mind-blowingly, some enzymes are even faster than this, so-called 'better than kinetically perfect' and how they manage their astounding speed is one of biology's great unsolved problems.
Some other cool example of proteins: Proton pumps in your stomach, which carry individual protons into your stomach to make acid. Photosystems 1 and 2 in plant chloroplasts, which juggle electrons between each other and weave sunlight into sugar, forming the basis of the whole earth's food chain.
Congratulations, in advance!!!
The other day I reflected over the lack of knowing how these foldings work; I recalled some tv program for the 70s that had identified this as a big issue back then Voila, today we have a working progress.
Nobel Prize material, indeed!!!
chains of amino acids that fold spontaneously into a precise conformation, time after time
I've seen this happen in many Japanese movies before, the Japanese do have a way to make proteins always hit the same spots from a distance.
Ok, I'll have 500g of Bovine Psoas Major proteins, preferably with some cured porcine abdominal protein wrapped around it.
Tiller's Rule: Never use a word in written form that you've only heard and never read. You will end up looking foolish.
...has designed five proteins from scratch that fold reliably into predicted conformations.
Let me me guess:
One is a potent carcinogen. :p
One causes deadly priapism
One causes thick hairgrowth... inside your body.
The two others are considered really dangerous.
Forget frankenmeat cow, now you can make meat that's never existed in nature. "Hmmm... I call this... Zerg Steak."
Here it comes!
The guy who said the election was rigged won the presidency with the second-most votes.
Only terrorists print proteins, because they can could be used to create outbreaks of bovine spongiform encephalopathy
http://en.wikipedia.org/wiki/Prion
I used to work in a protein engineering lab that collaborated extensively with Baker's lab. Let me be the first to say the quality of work coming out of there is outstanding. Protein engineering is incredibly difficult and their Rosetta software (protein folding again) is pretty much essential (yeah yeah, there's other software and rosetta has flaws, like not taking charged amino acids into account, but really its the best we have) -- even more so than pymol for any design you'd be doing.
This is the second large break through coming from them in the past few years. The other one was designing enzyme that performed a totally novel reaction. Details here: http://www.sciencemag.org/content/329/5989/309 . I really can't stress how big of a deal this is for designed (chemical) molecules. Even if the reaction wouldn't have happened under normal conditions or without causing decomposition to the rest of the molecule, you can make an enzyme that will do it for you.
This study should help the creation process, generally directed design runs into a lot of problems with proteins that no longer fold. Being able to determine computationally what has a chance of working would greatly speed up the process. Beyond that congrats to the lab and one of the most hands on, in the science PIs I know
Given the rapid pace of new and amazing announcements, have we reached the knuckle in the exponential curve of scientific development?
This is awfully cool!
According to the article, they used Rosetta@home for some predictions. I wonder if they've also tried fold.it, especially since that project is also out of U of Washington.
"Two things are infinite: the universe and human stupidity, and I'm not sure about the former." -- Albert Einstein
I work in the Baker Lab, and work like this relies on the processing cores of thousands of people around the world. The structure of every protein designed in this paper were determined using a computer very much like the one you're probably using to read this. If you would like to donate your unused CPU cycles, it would be a great (and direct) help for advancing the field of protein design and structure prediction -- please visit http://boinc.bakerlab.org/rosetta/ to sign up. And if you're interested in helping out to develop new strategies for protein structure prediction, try fold it (http://fold.it/portal/)