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First of all, excellent experiment. I love the big turnout and significance of the results. That said...
Methinks it could be more a total mash time thing (105/90 minutes steps vs. 80/60 single, with/without mashout times included) than an actual difference between mashing processes. Or maybe a bit of both. I have this theory (or isn't it fact?!) that enzymes work at any temperatures until they get denatured. So all that time at 113 and 131 F for the step mash beer? Yeah, the alphas and betas are chugging along nicely for a whole hour, and then later for another 30-45 minutes again at higher temps. Compare that with just 60-80 total and there likely could be a difference from the total time, not just the process. That's my thoughts on this. More than one variable so it's tough to nail down exactly why there's a difference.
But, good to know that regardless of variables, the mashing process or time or both probably do make differences. Makes sense.
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Just a quick look at McGregor, Cereal Chem. 55(5):754-765, shows that alpha-amylase is 50% active at 35 deg C, and maximally active at about 60C, after which the enzyme is quickly denatured (i.e. even though it is maximally active its stability is crap at that temp). It's a safe assumption something similar holds true for beta. In other words, your theory is absolutely correct.