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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."
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]
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"!
Next step: understand how specific conformations perform their magic in accelerating chemical reactions by factors of trillions so we can design custom enymes.
Because, unless your're His Noodliness, you have to start out small. We can make DNA of reasonable length but we don't know how to create a sequence that will cause a protein to fold in a specific pattern to it will have a specific function and not act like a disorganized blob of glop.
You want to be the whole spaghetti, not just the stuff tossed out in the sink.
Faster! Faster! Faster would be better!
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?
What vanity is there in doing it right in the first try? It is a very interesting achievement, one that relies not on the blind luck of evolution but on the application of a limited set of rules.
If evoultion worked like this, perhaps our retinas wouldn't be turned inside out as the currently are (for example).
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.
Impressive is a subjective quality: while you may only find a whale-size elephant impressive, I find it quite impressive that someone has managed to do from scratch what evolution might only do after a relatively long time and probably with lots of inefficiencies and side-effects.
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
What vanity is there in doing it right in the first try? It is a very interesting achievement, one that relies not on the blind luck of evolution but on the application of a limited set of rules.
If evoultion worked like this, perhaps our retinas wouldn't be turned inside out as the currently are (for example).
Without even questioning your unsubstantiated claim that our retinas are turned inside out, are flawed and could be better designed - isn't what's "right" or "correct" here also subjective by your own argument? Why is it that we can so easily critique something we don't fully understand, and the have the arrogance to presume, based on our limited understanding that it could be made better, without actually demonstrating it?
If anything, an evolutionist should argue that the best design to gaurantee our survival is what we currently have because all the other randomly generated attempts failed.
Impressive is a subjective quality: while you may only find a whale-size elephant impressive, I find it quite impressive that someone has managed to do from scratch what evolution might only do after a relatively long time and probably with lots of inefficiencies and side-effects.
What can I say, you're either easily impressed or helplessly delusional. Even the article presents the same argument and tries to justify their work to make it seem less vain:
One might wonder how designing a new protein from scratch could be better than starting with natural proteins, given the head start that nature has in evolving effective functions and stable conformations. In fact, evolution has honed the structures of many proteins so precisely that it can be difficult to get the backbone to budge into another conformation to accommodate a new function.
...unsubstantiated claim that our retinas are turned inside out...
What would you call a retina that has the photoreceptors hidden behind the axons and the blood vessels so the blood vessels and the axons are inside the sphere area corresponding to the photoreceptors? Compare it to the octopus eye which has no extra layers between the light and the photoreceptors.
...are flawed and could be better designed - isn't what's "right" or "correct" here also subjective by your own argument?
They are flawed since they could be much more efficient "just" by having the layers in the right order, as in cephalopods. It just happens that evolution didn't have a plan at all (that's what evolution does, anyway) and, when animals needed better night sight, patches like reflective areas in the front of the eye had to be evolved, because turning back and redoing it all again wasn't an option any more.
If anything, an evolutionist should argue that the best design to gaurantee our survival is what we currently have because all the other randomly generated attempts failed.
It is the least worst that survived, not the best. If it was the best we would copy it down to the details, and I know of no artificial camera that puts anything between the lens and the photosensible material that isn't really needed there. At least, I don't know of any camera with a blind spot designed into it.
What can I say, you're either easily impressed or helplessly delusional. Even the article presents the same argument and tries to justify their work to make it seem less vain
I'm sure qualifying people so easily that helps your arguments a lot. Anyway, I find it impressive because it certainly isn't easy: otherwise someone would have probably done it decades ago. And, if the article tries to make it less vain, please tell me, why on Earth did the previous AC (I can't tell whether it was you) write this?:
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"?
Either the article is celebrating an achievement and the quote is right, or it isn't as you write now and the quote was wrong, your choice :)
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.
You don't really seem to understand evolution, nor random search. Go study and come back.
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.
WTF?
A fool throws a stone into a well and a thousand sages can not remove it.
Forget frankenmeat cow, now you can make meat that's never existed in nature. "Hmmm... I call this... Zerg Steak."
You should be careful about the lies you spread around. One of these days, the great Invisible Pink Unicorn will get you.
Get free satoshi (Bitcoin) and Dogecoins
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
Mark my words, it's only a matter of time before someone discovers that what were previously thought to be imperfections in the design of the eyes of vertebrates actually make it far superior to the octopus eye....the research just hasn't been done yet. Just like the so call "junk DNA" that evolutionist of the 1990s were leaning on, insisting that it supports Darwinism. Now the ENCODE project has found much of what was previously considered junk DNA provide important functions (albiet not protien coding).
So, be careful what you accept as science fact. I respect science and research but some of this stuff is just the opinion of arrogant men who are obsessed with their own ideas of how things should be (i.e. they are delusional). Remember Fred Hoyle?
--- we admit that natural things have a design, yet we deny there being a designer....oh the vanity of man.
Mark my words, it's only a matter of time before someone discovers that what were previously thought to be imperfections in the design of the eyes of vertebrates actually make it far superior to the octopus eye...
Excuse me if I don't hold my breath. I'm not an octopus, mind you ;)
I respect science and research but some of this stuff is just the opinion of arrogant men who are obsessed with their own ideas of how things should be (i.e. they are delusional). Remember Fred Hoyle?
What would you need to not consider it "just the opinion of arrogant men"? Actually, I think that considering the human/mammal eye to be suboptimal shows more humbleness than arrogance, at least if you consider the millennia during which humans have asserted their being at the cusp of everything. And then it was discovered that the Earth wasn't the center of the solar system, that the solar system wasn't the center of the universe... I really think that finding out that the human is inherently suboptimal is quite humble. But that's just my opinion.
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/)