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Biotech Science

Proteins Made To Order 51

Posted by samzenpus
from the molecules-to-go dept.
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."
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Proteins Made To Order

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  • I want them to synthesize a fully functioning Marylin Monroe to go with my 3D printed vintage sports car.
    • 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.

      Barring certain genetic anomalies, it should be pretty easy for any husband and wife team to produce protein sequences that result in predicted conformations.

      • I want them to synthesize a fully functioning Marylin Monroe to go with my 3D printed vintage sports car.

        Barring certain genetic anomalies, it should be pretty easy for any husband and wife team to produce protein sequences that result in predicted conformations.

        Sex can produce cars?

    • I love the juxtaposition of your comment and your sig.
  • by srussia (884021) on Friday November 09, 2012 @03:40AM (#41929951)
    FTFA: "The work was spearheaded by husband-and-wife team Nobuyasu Koga and Rie Tatsumi-Koga"

    A centuries-old tradition of origami!
    • by drinkypoo (153816)

      A centuries-old tradition of origami!

      Not to mention the long and hallowed tradition of husband-and-wife teams engaging in protein-folding experiments...

  • by Anonymous Coward

    Next step: understand how specific conformations perform their magic in accelerating chemical reactions by factors of trillions so we can design custom enymes.

  • hello -- (Score:5, Informative)

    by GPierce (123599) on Friday November 09, 2012 @04:46AM (#41930143)

    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.

    • Re: (Score:2, Interesting)

      by Anonymous Coward

      If this happens this could open up a new era in medicine.
      It is literally *the* cure for hiv , cancer and just about everything else. Specific proteins can be created to attach to and kill exactly just about anything , it's the perfect artificial immune system.
      The gloomy side of this is that it will also open up the door for new weapons. One could theoretically build proteins designed to kill exactly one individual potentially without leaving much of a trace to the untrained eye.

    • by mapkinase (958129)

      Shaping is nothing in proteins. Function is everything.

  • by Anonymous Coward on Friday November 09, 2012 @06:30AM (#41930497)

    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.

    • by Anonymous Coward

      Photosynthesis is achieved by having a very specialized enzyme that works like a workshop bench. It clamps down the hydrogen bonds of the H2O molecule and literally snips off the hydrogen atoms using the energy from several UV photons. All done using the electrical charges of chemical bonds and free electrons.

    • by mcgrew (92797) *

      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... thiotimoline is an enzyme? Biochemist Dr. Asimov was wrong about its composition?

    • I remember hearing that DNA polymerase runs so fast along DNA that if it were a train, and the base pairs were railroad ties, it would be moving something like a thousand miles an hour. And it would be duplicating the train tracks nearly perfectly as it did so.
    • Re: (Score:2, Informative)

      by Anonymous Coward

      I don't think OP did a great job of explaining kinetic perfection, so I'll try to expand on it.

      Firstly, I've generally heard it referred to as catalytic perfection, not kinetic. Regardless, it means that

      1) every enzyme-substrate collision is productive, that is, generates a product and
      2) the reaction happens in less time than the enzyme and substrate can find each other in solution.

      This means that the "limiting reagent" of the reaction is the diffusion speed of the enzyme and substrate - if enzyme and subst

  • 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.

  • by Type44Q (1233630) on Friday November 09, 2012 @08:17AM (#41930967)

    ...has designed five proteins from scratch that fold reliably into predicted conformations.

    Let me me guess:

    One is a potent carcinogen.
    One causes deadly priapism [wikipedia.org]
    One causes thick hairgrowth... inside your body.
    The two others are considered really dangerous. :p

  • by Anonymous Coward on Friday November 09, 2012 @09:41AM (#41931553)

    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

  • This is awfully cool!
    According to the article, they used Rosetta@home for some predictions. I wonder if they've also tried fold.it [fold.it], especially since that project is also out of U of Washington.

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