tag:blogger.com,1999:blog-37148773.post897201172975862568..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Enzyme Efficiency: The Best EnzymeLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-37148773.post-14642526679883475902008-11-12T18:01:00.000-05:002008-11-12T18:01:00.000-05:00athel says,An additional point is that we are real...athel says,<BR/><BR/><I>An additional point is that we are really being asked to be impressed at how slow the uncatalysed reaction is, not how fast the catalysed reaction is. But who cares about that?</I><BR/><BR/>I do.<BR/><BR/>It's hard to get students to learn this conceptual stuff. That's why I'm always looking for examples to illustrate the difference between so-called "spontaneity" (deltaG) and rate.<BR/><BR/>This looks pretty good to me even with the qualifications noted by dk. In the textbook I'll say that the rate is only an estimate.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52407132466280418162008-11-12T07:26:00.000-05:002008-11-12T07:26:00.000-05:00I agree with most of DK's comments, so I won't rep...I agree with most of DK's comments, so I won't repeat the arguments. The main one where I have reservations is <BR/><BR/><I>a common (and severe) mistake was made by applying equal weights to the data spanning 3 orders of magnitude.</I><BR/><BR/>Effectively the authors have assumed uniform lognormal errors, approximately the same as saying that they are uniform in coefficient of variation. This may often be closer to the truth than the more usual assumption that they have unform variance. Of course, the important point is that the weighting should be based on the real (preferably measured, but that means virtually never!) error distribution, not on whatever is most convenient for calculation. The only case that I know of where an experimentally determined distribution of error in a enzyme in an experiment turned out to be close to uniform variance was the original study of Lineweaver and Burk way back in 1934. However, don't look at the paper that everyone refers to but few have read; look at the one they wrote in the same year with W. E. Deming (a real statistician) in <I>J. Amer. Chem. Soc.</I> <B>56</B>, 225-230.<BR/><BR/>An additional point is that we are really being asked to be impressed at how <I>slow</I> the uncatalysed reaction is, not how fast the catalysed reaction is. But who cares about that? Humans learned how to accelerate very slow processes by many orders of magnitude at least 4000 years ago (for example, building of the pyramids or Stonehenge -- large chunks of rock move exceedingly slowly, if at all, in nature) , but they only learned how to double the rate of a fast process in the past couple of centuries (for example the speed of a car compared with that of a galloping horse).Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75635074771993795412008-11-11T21:33:00.000-05:002008-11-11T21:33:00.000-05:00Into the textbook it goes Doubt it. 1. Described ...<I> Into the textbook it goes </I> <BR/><BR/>Doubt it. <BR/><BR/>1. Described is a perfectly mediorce enzyme, with kcat/Km of only ~ 3e6. There are a number of enzymes that are 100X better catalysts, with kcat/Km > 2e8. <BR/><BR/>2. The big number that is supposed to awe everyone is based on *extrapolation* of the experimentally derived spontaneous rate. <BR/><BR/>3. The Fig.3's legend says that a linear fitting was used for the Arrhenius plot. In other words, a common (and severe) mistake was made by applying equal weights to the data spanning 3 orders of magnitude. Jeez, and I thought these days every Biochem 101 student is taught to NOT ever derive anything from linearized plots! That no estimated standard deviations of the fit's parameters are mentioned anywhere in the paper is only all too telling... <BR/><BR/>4. Considering the above, it's anyone guess how close to reality the extrapolation from >100C down to 25C is. (And that is even *assuming* that Arrhenius plot is linear over the entire range of 150-20C - which may not be true; life is full of nonlinear Arrhenius plots). <BR/><BR/>5. On top of the problems above, the study did not use the actual sustrate. It used a much smaller compound that is part of the porphyrinogen. This had to do with obvious experimental limitations but it is far from given that PAA and porphyrinogen have identical sponataneous rates of decarboxylation! At a minimum, a full quantum mechanics calculation of the electron density distribution should have been carried out and provided to prove that it is reasonable to assume the near equivalence. (That's not difficult to do these days but it was evidently not done). That the macrocycle ring has absolutely no influence on the chemistry of pyrroles is a very dubious assumption, IMHO. <BR/><BR/>All in all, a shaky ground for any quantitative claims. Seems like a typical PNAS paper from old times.Anonymousnoreply@blogger.com