Kinetic folding experiment

The rabbit FruA discriminates the enantiomers of its natural substrate with a 20 1 preference for D-GA3P (12) over its L-antipode [202], Assistance from anionic binding was revealed by a study on a homologous series of carboxylated 2-hydroxyaldehydes which showed optimum enantioselectivity when the distance of the charged group equaled that of 12 (Scheme 15, Fig. 11) [299], The resolution of racemic substrates is not, however, generally useful since the kinetic enantioselectivity for nonionic aldehydes is rather low [202], 3-Azido substituents (69) can lead to an up to 9-fold preference of enantiomers in kinetically controlled experiments [300] while hydroxyl (70 preference for the... 

Ubiquitin has been the subject of a number of experimental studies as it is a small and soluble protein without disulfide linkages. The protein has a well-defined and packed hydrophobic core. There are a number of kinetic folding studies on this system, in addition to a high resolution crystal structure. 2D NMR studies of a partially unfolded form of the protein in 60% methanol indicate that approximately one-half of the molecule contains dismpted but native-like structure, while the other half is unstmctured and/or contains non-native structure. The interpretation of hydrogen-exchange experiments have led to the conclusion that this state is native-like. ... 

The first set of experiments was conducted in methanol. The substrate concentration was varied from 15 to 50 mM at a 200 pM concentration of 1 for the determination of kinetic parameters for the transformation of 8 into 9. The catalytic rate constant was determined to be 0.04 min and the Michael constant was determined to be 40 mM at 30°C. The rate constant is comparable to those reported for other dinuclear Cu(ll) complexes with a comparable Cu -Cu distance of 3.5 A, but about one magnitude lower than those observed for complexes with a shorter intermetallic distances (12-14), e.g. 2.9 A (kcat = 0.21 min ) (12) or 3.075 A (kcat = 0.32 min (13). The rate constant Aion for the spontaneous (imcatalyzed) oxidation of 8 into 9 was determined to be 6 x 10" min and corresponds to the oxidation without catalyst under otherwise identical conditions. The rate acceleration (Arca/Aion) deduced from these values is 60,000-fold. 

The /) values can be determined formally only through careful experiments. Significantly, however, /) values are needed only for species whose concentrations change under the conditions of interest for other species, the quantities can be folded into the corresponding kinetic constant, or the kinetic constant and rate constant. For species whose concentrations are likely to change, such as the reaction substrates, /3 is commonly taken to be one, in the absence of contradictory information... 

The mechanistic basis of 3 and 4 is a double application of the argument used for the YES operation with 1. Each receptor in 3 is capable of launching a PET process if the lumophore is powered up by ultraviolet excitation. In other words, the fluorescence of the 9-cyanoanthracene unit is efficiently quenched by either the amine or the 1,2-dioxybenzene group within the benzo-15-crown-5 ether unit. These quenching processes are predictable from thermodynamic calculations or from related bimolecular quenching experiments in the literature. The small separation of the amine from the lumophore ensures rapid PET kinetics. On the other hand, the presence of four bonds between the benzo-15-crown-5 ether and the lumophore is probably responsible for the incomplete quenching seen between this pair. No information is yet available regarding possible folded conformations of 3. 

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