Limits...
Enzyme-specific activation versus leaving group ability.

de Beer RJ, Bögels B, Schaftenaar G, Zarzycka B, Quaedflieg PJ, van Delft FL, Nabuurs SB, Rutjes FP - Chembiochem (2012)

Bottom Line: Enzyme-specific activation and the substrate mimetics strategy are effective ways to circumvent the limited substrate recognition often encountered in protease-catalyzed peptide synthesis.A key structural element in both approaches is the guanidinophenyl (OGp) ester, which enables important interactions for affinity and recognition by the enzyme--at least, this is usually the explanation given for its successful application.In this study we show that leaving group ability is of equal or even greater importance.

View Article: PubMed Central - PubMed

Affiliation: Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.

Show MeSH
Molecular modeling of OGp analogues in trypsin. Hydrogen bonding interactions to functionally important amino acids in the trypsin active site are shown for A) arginine, B) OGp, C) OGb, D) O3G, and E) OAb. The space occupied by the arginine side chain is indicated in blue.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3569868&req=5

fig01: Molecular modeling of OGp analogues in trypsin. Hydrogen bonding interactions to functionally important amino acids in the trypsin active site are shown for A) arginine, B) OGp, C) OGb, D) O3G, and E) OAb. The space occupied by the arginine side chain is indicated in blue.

Mentions: The Z-Gly-OGp ester (Figure 1 B) could be easily docked in the active site of trypsin, in a similar way to the arginine side chain (Figure 1 A), in agreement with previous findings.[7] The guanidino group made the equivalent crucial interaction with Asp189 in the S1 pocket and, additionally, formed hydrogen bonds with Ser190 and Trp215. Furthermore, the substrate carbonyl was nicely located in the oxyanion hole. The docking poses of the benzylic esters Z-Gly-OGb and Z-Gly-OAb were less optimal, even though the carbonyl groups were located in the oxyanion hole. Figure 1 C shows that OGb slightly extended beyond the volume occupied by the arginine side chain as a result of the additional carbon atom, whereas OAb (Figure 1 E) had to adopt a somewhat distorted conformation to be located in the oxyanion hole while simultaneously retaining interaction between the amidinium group and Asp189. The aliphatic Z-Gly-O3G analogue (Figure 1 D) perfectly mimicked the side chain of arginine, thus achieving hydrogen-bond interactions with Asp189, Ser190, and Tyr217. The oxyanion hole residues Gly193 and Ser195 were in the correct position to stabilize the carbonyl of the ester. Z-Gly-NGp showed a binding mode similar to that of Z-Gly-OGp.


Enzyme-specific activation versus leaving group ability.

de Beer RJ, Bögels B, Schaftenaar G, Zarzycka B, Quaedflieg PJ, van Delft FL, Nabuurs SB, Rutjes FP - Chembiochem (2012)

Molecular modeling of OGp analogues in trypsin. Hydrogen bonding interactions to functionally important amino acids in the trypsin active site are shown for A) arginine, B) OGp, C) OGb, D) O3G, and E) OAb. The space occupied by the arginine side chain is indicated in blue.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3569868&req=5

fig01: Molecular modeling of OGp analogues in trypsin. Hydrogen bonding interactions to functionally important amino acids in the trypsin active site are shown for A) arginine, B) OGp, C) OGb, D) O3G, and E) OAb. The space occupied by the arginine side chain is indicated in blue.
Mentions: The Z-Gly-OGp ester (Figure 1 B) could be easily docked in the active site of trypsin, in a similar way to the arginine side chain (Figure 1 A), in agreement with previous findings.[7] The guanidino group made the equivalent crucial interaction with Asp189 in the S1 pocket and, additionally, formed hydrogen bonds with Ser190 and Trp215. Furthermore, the substrate carbonyl was nicely located in the oxyanion hole. The docking poses of the benzylic esters Z-Gly-OGb and Z-Gly-OAb were less optimal, even though the carbonyl groups were located in the oxyanion hole. Figure 1 C shows that OGb slightly extended beyond the volume occupied by the arginine side chain as a result of the additional carbon atom, whereas OAb (Figure 1 E) had to adopt a somewhat distorted conformation to be located in the oxyanion hole while simultaneously retaining interaction between the amidinium group and Asp189. The aliphatic Z-Gly-O3G analogue (Figure 1 D) perfectly mimicked the side chain of arginine, thus achieving hydrogen-bond interactions with Asp189, Ser190, and Tyr217. The oxyanion hole residues Gly193 and Ser195 were in the correct position to stabilize the carbonyl of the ester. Z-Gly-NGp showed a binding mode similar to that of Z-Gly-OGp.

Bottom Line: Enzyme-specific activation and the substrate mimetics strategy are effective ways to circumvent the limited substrate recognition often encountered in protease-catalyzed peptide synthesis.A key structural element in both approaches is the guanidinophenyl (OGp) ester, which enables important interactions for affinity and recognition by the enzyme--at least, this is usually the explanation given for its successful application.In this study we show that leaving group ability is of equal or even greater importance.

View Article: PubMed Central - PubMed

Affiliation: Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.

Show MeSH