The generation of enzymes to catalyze specific reactions is among the
May 16, 2017
The generation of enzymes to catalyze specific reactions is among the more challenging problems facing protein engineers. Biolabs. Ultrapure dNTPs were obtained from Boehringer Mannheim. Agarose for analytical gel electrophoresis was obtained from Kodak. Agarose for preparative gel electrophoresis was obtained from FMC. Purified scytalone dehydratase 2 3 5 every chemical reaction seems unfeasible. Levinthal (21) has pointed out that for any 100-aa protein to sample every possible conformation it would take 1027 years for the protein to fold into the correct NVP-BGJ398 conformation. Similarly for nature to explore all the sequence space available to a 100-aa protein would require production of 20100 different proteins. If only 1 μg of each variant was produced starting materials with a mass of 1.27 × 10124 g greater than the mass of the earth (5.98 × 1027 g) would be required. It seems likely therefore that in the development of proteins and specifically enzymes nature has recruited motifs and domains from other functions and retooled them to change specificity and chemistry. The α/β barrel is certainly one such exemplory case of a proteins scaffold that acts as the construction for chemically different enzymatic reactions that appear to possess evolved through adjustments in key proteins within the energetic site (22). Through the use of two protein that participate in the α + β flip group NTF2 and scytalone dehydratase we’ve sought to make a exclusive biocatalyst by mimicking procedures that people believe happen in nature specifically the retooling of energetic sites for different catalytic features. Our goal is certainly to minimally reconfigure the proteins scaffold to confer both NVP-BGJ398 substrate binding and enzymatic activity upon this fragment. Evaluation from the crystal framework of NTF2 uncovers the current presence of a hydrophobic pocket in the same area as the hydrophobic active site of scytalone dehydratase and binds to the small molecular excess weight G-protein Ran (23). A phenylalanine residue of Ran binds into the hydrophobic pocket of NTF2. Because of NVP-BGJ398 the similar overall structure and presence of an appropriately placed hydrophobic pocket in NTF2 we reasoned that it should be possible to decorate the hydrophobic pocket of NTF2 with residues from scytalone dehydratase that confer substrate binding and catalysis. Surprisingly the wild-type NTF2 was found to be capable of binding the tight-binding inhibitor of scytalone dehydratase even though difference in Kd values is a factor of 106 disfavoring NVP-BGJ398 binding to NTF2. The conversation of the inhibitor with NTF2 is most likely a consequence of its hydrophobic nature rather than a specific conversation with the protein. By decorating the hydrophobic pocket of NTF2 with residues that should confer substrate binding and catalysis we were able to observe a value for kcat/Km between 0.47 × 10?6?μM?1?min?1 and 2.6 × 10?6?μM?1?min?1 toward DDBO. If we presume the binding of inhibitor and DDBO to our construct parallels their affinity for scytalone dehydratase the Km for DDBO would be greater than mM. We suspect that the Km for DDBO is indeed in that range because simulations of the kinetic assay converge to a span of Km values from 0.8 to 3 500 mM. Consequently kcat is usually minimally a value of 150 over background and most likely higher. Given that wild-type NTF2 possess no scytalone dehydratase activity and appears to be unable to bind the tight-binding inhibitor with high affinity it is remarkable that we happen to be able to convert the NTF2 scaffold into an enzyme. This result clearly indicates the applicability of retooling protein scaffolds into catalytically active proteins able Cd63 to take action on substrates previously not associated with that scaffold. Mutagenesis studies of the serine protease substilisin parallel the work described here (24). Replacement of the three important catalytic residues with alanine lowered kcat by a factor of 107 with little effect on Km. However this protein was still capable of a rate acceleration of 2.7 × 103 above the background rate of hydrolysis. The most dramatic loss of activity was with the first mutation a drop in.