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For an example of the design and functional characterization of an antibody binding site that was designed to exhibit broad specificity at the α-substituent of the amino acid substrate see: Tanaka, F., Kinoshita, K., Tanimura, R., Fujii, I. J. Am. Chem. Soc. 1996, 118, 2332-2339. The relaxation of substrate specificity at this position was accomplished by substituting the α-substituent with the linker.
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The substrate corresponding to 1p is 1. The hydrolysis of phenyl acetate, the substrate that corresponds to the phosphonate, 11p, was not catalyzed by 17E8 (data not shown)
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The substrate corresponding to 1p is 1. The hydrolysis of phenyl acetate, the substrate that corresponds to the phosphonate, 11p, was not catalyzed by 17E8 (data not shown).
-
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22
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0345318757
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The substrate 13 was prepared as a 1:1 mixture of the cis and trans isomers whereas 12 was purely trans
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The substrate 13 was prepared as a 1:1 mixture of the cis and trans isomers whereas 12 was purely trans.
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3), respectively (see refs 40 and 41)
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However, the energetic cost needed for the antibody to constrain the side chain is not realized with the fixed rotamer mimick (13). This conformer is about 3.5 kcal/mol higher in energy than the staggered, low-energy conformer (see refs 40 and 41). Thus, structurally constraining the side chain should allow for this energy to be expressed in greater transition state stabilization. The decrease in activity (Tables 1 and 3) for 13 compared to 5 is most likely a result of the fact that the eis isomer does not resemble the bound rotamer precisely due to changes in the hybridization at the δ and γ carbons as well as differences in the dihedral angle between 13 and the actual bound rotamer. The alkene side chain is also less hydrophobic (than 5), thus raising the desolvation cost for binding. The fact that 14 was also a substrate suggests that the rotameric requirement is only important for the torsion angle defined by carbons Cb-Ce
-
However, the energetic cost needed for the antibody to constrain the side chain is not realized with the fixed rotamer mimick (13). This conformer is about 3.5 kcal/mol higher in energy than the staggered, low-energy conformer (see refs 40 and 41). Thus, structurally constraining the side chain should allow for this energy to be expressed in greater transition state stabilization. The decrease in activity (Tables 1 and 3) for 13 compared to 5 is most likely a result of the fact that the eis isomer does not resemble the bound rotamer precisely due to changes in the hybridization at the δ and γ carbons as well as differences in the dihedral angle between 13 and the actual bound rotamer. The alkene side chain is also less hydrophobic (than 5), thus raising the desolvation cost for binding. The fact that 14 was also a substrate suggests that the rotameric requirement is only important for the torsion angle defined by carbons Cb-Ce.
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47
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0344887575
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The substrates 6 and 11 (and phosphonates 6p and 11p) were not included in the correlations because we believe that these molecules could not be accommodated without changes in pocket structure or binding mode, making the analysis of these compounds ambiguous
-
The substrates 6 and 11 (and phosphonates 6p and 11p) were not included in the correlations because we believe that these molecules could not be accommodated without changes in pocket structure or binding mode, making the analysis of these compounds ambiguous.
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