Field of Science

New place, new view, slow reactions and the origins of life
I have been unable to blog for the past few days because I was busy moving to Chapel Hill for a postdoc at UNC Chapel Hill. I am very excited about this move and my upcoming research which is going to involve protein design and folding. Regular blogging will resume soon. Until then, happy holidays, and I will leave you with the following interesting paper published by a group from my new institution.

One of the abiding puzzles in the origin of life is to explain how life arose in the relatively small amount of time it had to evolve on the planet. From a chemical perspective, this entails explaining how especially slow chemical reactions could have contributed to the complexity of life. In a new paper in PNAS, a group from UNC suggests part of a possible solution to the puzzle by demonstrating that slow reactions especially are accelerated by temperature much more than fast reactions. Recall from college physical chemistry that the rate of a typical reaction roughly doubles with ten degree rise in temperature. As the authors note, this bit of textbook wisdom is off the mark when it comes to many important reactions and needs to be appended.

They look at certain important reactions like the hydrolysis of phosphate monoesters and find that these reactions are accelerated not two or a few fold but many million fold with a rise in temperature. The increase in rate would have been significant especially under the hot, primordial conditions present on earth during its early days. Now this acceleration is free-energetic and basically corresponds to a favorable change in either the entropy or the enthaply of activation. The authors measure both these variables and find that the crucial change is in the enthalpy. It's interesting to note that a favorable change in the enthalpy would entail forming stronger interactions including hydrogen bonds between substrate and enzyme, and this is exactly the kind of process you would imagine happening during the optimization of biomolecular interactions during evolution. In fact, recent research suggests that this process of optimizing enthalpy is also synthetically mirrored during drug discovery. The authors end by explaining why a catalyst that impacted enthalpy rather than entropy favorably would have had a selective advantage in rate acceleration as the environment later cooled (and entropy became unfavorable).

Amusingly, the paper has come under criticism from some unexpected quarters, from none other than folks from the infamous 'Discovery' Institute which is funded and run by creationists. In the view of these esteemed 'scientists', the paper provides no evidence that the slow reactions which were accelerated were in fact ones which were important during the origin of life. The DI crowd seems to have fundamentally misjudged the nature of origins of life research; it's more speculative than many other fields but still remains scientific. More importantly, the criticism seems to have completely missed the fact that the general hypotheses proposed by the authors- that all slow reactions could have been vastly accelerated by temperature on a hot primordial planet- is independent of the exact nature of these reactions which may or may not have contributed to life's origins. As usual, miss the forest for the trees.

Stockbridge, R., Lewis, C., Yuan, Y., & Wolfenden, R. (2010). Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes Proceedings of the National Academy of Sciences, 107 (51), 22102-22105 DOI: 10.1073/pnas.1013647107


  1. Torbjörn Larsson, OM4:58 AM, December 23, 2010

    I'm quite happy with the paper, as it gives a simple model that forces enzymes and putatively metabolism onto a probiotic to protobiotic transition. It wouldn't be a one chance pathway on many or most habitable zone planets either, since their accretion/migration phase would have a tail end influx of impactors too, FWIW resulting in millennium or longer local hot zones.

    [Merely a layman here. But since the Nuvvuagittuq rocks imply that there could have been an organic sulfur cycle going back before our own Last Heavy Bombardment, and newer models suggest a Goldilocks cellular survival zone ~ 1 km into the crust, I now favor the likelihood that the protobiotic attempt that "caught" was earlier and then likely the Earth original cooling. However, multiple possible pathways is certainly a boon.]

    Moreover, it notes that the RNA world fossil of the ribosome core is more an assembly engine than an (enthalpic) enzyme. This fits nicely with the discovery that the ribosome center is a water trap with water molecules acting as both actuators and in enzymatic oxyanion function ("catalytically favorable both in terms of activation enthalpy and entropy").

    The post note of the hydrogen bond interaction is interesting. Would that mean that the case for water as the preferred cellular liquid got even stronger? I would like to think so.

  2. Torbjörn Larsson, OM5:01 AM, December 23, 2010

    I wanted to add that the ribosome low temperature range acquired function is a must (being an RNA at the core and all), but that the paper really points out how the function have all the hallmarks for this. (Maybe they said as much, I can't remember as I'm writing this.)

  3. UNC-Chapel Hill is a great place! Congratulations! As a synthetic person who spent some time there, it's a great department, with a very "open door" policy and no real fiefdoms. Two thumbs up!

  4. Torbjörn, thanks for the comments and the link. UNC guy: Ditto! Julie, I hope that exclamation mark is supposed to convey positive feelings!

  5. nothing but. how exciting to start something new in such a thought-provoking environment. Hope it yields many posts to come. I have enjoyed all so far.

  6. Ran across the paper in my reading of PNAS. 2011 is going to be the year of serious PChem study. I did audit a PChem course a while ago but it ws pretty basic. I'll save the paper for then.

    I'd like some recommendations for the most current book (or review) on protein folding.

    Happy new year to all



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