The Veirfication For Protein Quantum Folding Theory From Evolutionary History Of Protein Architecture

The large molecules lie in the “border territory” between the “quantum” and the“classical”. To which extent one should employ the classical or quantum-mechanicalmethods in describing their behavior is an open issue. Protein folding mechanism iscommonly studied by use of classical molecular dynamics (MD) simulation as a maintheoretical tool. However, atomic and molecular obey quantum regular in view of mo-modern physics. Luo and researchers put forward protein quantum folding theory in recentyears. Protein folding rate deduced from quantum conformational transition. A statisticalformula for the prediction of protein folding rate was proposed based on quantum foldingtheory. The statistical comparisons of the temperature dependence of folding rate for16typical proteins and the folding rates for65two-state proteins were carried out, and thetheoretical vs. experimental correlation coefficient was0.73. These results justify thefeasibility of protein quantum folding theory. Of course, it still need more evidence toverify this theory.We extended the model on the folding rate and make the statistical investigation ofthe folding rate for103single-domain protein, and the theoretical vs. experimentalcorrelation coefficient was0.77. Above all, we believe that the model on the folding ratecan forecast the unknown protein folding rate.Therefore, we studied evolution of protein structure in Folds level and Superfamilylevel. Here we propose that foldability is a constraint that crucially contributes toevolutionary history. Our results show a trend of folding rate increase from~3.8to~1.5billion years. But there is a trend of folding rate slower in~1.5billion years. This result isconsistent with Caetano-Anollés who estimated folding times for the present-day catalogof protein domains directly from their size-modified contact order.Interestingly enough, we provided an evolutionary event which is not found byCaetano-Anollés. We found a fluctuation of folding rate slower from~2.7to~1.5billionyears. This means protein structure became complex during this period of time. Studies byLake have shown that two single-membranes cell fusion into a double-membrane cell inabout2.5billion years ago. This is a big event in life evolution. Double-membranestructure has profoundly altered the evolution of life by providing endosymbionts necessary for the emergence of eukaryotes and by generating Earth’s oxygen atmosphere.Anbar also found oxygen geologically in this time.Our study demonstrates that, as protein topologies evolved and optimized to tightercompact, adding short range inter-aminoacid contacts etc, our results coincided withsomeone’s research like Caetano-Anolles, Lake, Anbar and so on, and also provided aninstance testing the protein quantum folding theory.