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generated structure with respect to domain 3 of the starting structure, after the two
domains have been optimally aligned. This is again different from sRMSD. D1RMSD
should be self explanatory. Given the noise in the data and the small size of the sample
we did not attempt to use sophisticated machine learning algorithms to further optimize
the parameters, leaving this instead to future work. The validity of the fitness function
will be demonstrated by the result of testing on four additional proteins in the following
section.
Results
Biotin Carboxylase
Acetyl-CoA carboxylase (ACC), found in all animals, plants, and bacteria, catalyzes the
carboxylation of acetyl-CoA to malonyl-CoA, the first committed step of fatty acid
synthesis. The first half-reaction is the formation of carboxybiotin which is catalyzed by
the Biotin carboxylase (BC) subunit.[102]
Pyruvate carboxylase (PC) is found in many eukaryotes and some prokaryotes. It plays a
role in gluconeogenesis, mediating the carboxylation of pyruvate to oxaloacetate. It has
three functional domains, of which biotin carboxylase (BC) is one. The half-reaction
catalyzed by BC is common to ACC and PC, although the second half-reaction catalyzed
by a different subunit differs from enzyme to enzyme depending on the substrate.[103]
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