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10 Responses to 2011-12-02

  1. DaFreak says:

    I never did any biology on a level this deep so this is all pretty new to me. To be honest, I prefer clean fundamental physics… these messy bundles you call proteins look awfully complicated when compared to particle/waves. ^^

    Great that we have smart minds working on this because it obviously is the future but the complexity of it all really scares me. Do you ever get used to it? That there are so many proteins who all have their own specific function is simply mind boggling.

  2. Rajini Rao says:

    That’s funny, Koen De Paus , proteins make perfect sense, it’s the physics that quickly becomes arcane to me. They are not messy at all..in fact, most of the protein is in one of two repeating structures: the so called alpha helix and the beta strand (ribbon). The strands stack together to make “sheets”. They are connected by tight or beta turns. Each of these structures is defined by precise angles that fall within an allowed space. Membrane proteins are my special interest, especially the ones that move ions. I can look at a protein and recognize the “fold”, they all have their own signature (good) looks. 🙂

  3. DaFreak says:

    “I can look at a protein and recognize the “fold”, they all have their own signature” – That is amazing and very nice to hear. I would have a lot of trouble seeing the trees through the forest. Definitely plan to read up on this more. All this talk of proton pumps and light activated signal transmission through kinetic energy is really setting my mind on fire. At this point we can only dream of creating such nanotechnology ourselves although advances are being made at breakneck speeds.

    I can proudly say I have been folding proteins as well…

    Actually my computer is doing that with Folding@Home but ssssjt 😉

  4. Kapil Ranade says:

    Dr Rajini Rao – what are your views on the ‘Foldit’ game that’s harnessing bright gamer kids to wiz through protein structure problems? (Had you linked an article on that before? I remember not.)

  5. Rajini Rao says:

    Kapil Ranade , I did post the story of the Nature paper using Foldit back in Sept. as did a lot of people on G+. FYI, I’m pasting my lede from that post here for you:

    In silico protein folding is a computer intensive effort with variable success. The trick is to predict how natural forces would drive a linear sequence of amino acids into a three dimensional structure of minimum energy. Protein folding algorithms frequently get targets trapped in false energy minima. David Baker of U Washington has been hosting a biennial competition that enlists gamers world wide to try their hand in generating plausible protein folds (http://fold.it/). This study reports that players used the online multiplayer Foldit game to solve the structure of an AIDS-like viral protease that had defied solution for 10 years. The authors attribute success to “human intuition” winning over automated methods. Imagine, with some guts and gore we could fully harness the awesome potential of gamers!

    Since then, I discussed the game with a respected biophysicist who works in the area..he was somewhat disparaging about the idea..he did have a point in that the gamers are not using any real understanding of the forces that shape proteins, they are just doing this randomly. However, it has merit because the players don’t know the “rules” so they may try something out of the box that could work. Also, at least it introduces people to the beauty of a biological molecule and some of them may well go on to learn a lot more.

  6. Lynn Ducalas says:

    u guys are sooo brilliant!

  7. I have 2 questions (i am citing them by an example) pls answer. Does the protein sequence of insulin carries the information that it has been formed only at the specific site in the body?? And this code/gene for this site specificity can be found comparing it with other proteins originating from the same part ………… like in this case glucagon

  8. Rajini Rao says:

    arunjyoti banik , you are referring to the promoter region of a gene that determines when and where that gene is transcribed (i.e., copied) from DNA. The protein sequence itself does not carry this information. The promoter is typically just upstream of the protein coding sequence.

  9. exactly but does this promoter region is conserved for all the proteins that are originating from that region????

  10. Rajini Rao says:

    There will be more than one tissue specific promoter for any region. But yes, each promoter can be recognized by their sequence.

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