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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.

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Structures of O3G variants and their docking poses. A) O3G=, B) O3G∇, C) O3GF2, and D) OTfe.
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fig02: Structures of O3G variants and their docking poses. A) O3G=, B) O3G∇, C) O3GF2, and D) OTfe.

Mentions: Inspection of the molecular model of trypsin with Z-Gly-O3G revealed that there is space in the binding pocket for the introduction of a small substituent (Figure 2), such as a methylene (O3G=) or two fluorides (O3GF2), which are weak and strong inductively electron-withdrawing groups, respectively. However, these modifications also create additional van der Waals interactions with the pocket, which by themselves can be a reason for increased affinity of the ester for the enzyme. To assess this effect, a cyclopropyl group was included (O3G∇), which was shown to fit in the binding pocket to make these additional interactions without altering the electronic properties.


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)

Structures of O3G variants and their docking poses. A) O3G=, B) O3G∇, C) O3GF2, and D) OTfe.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig02: Structures of O3G variants and their docking poses. A) O3G=, B) O3G∇, C) O3GF2, and D) OTfe.
Mentions: Inspection of the molecular model of trypsin with Z-Gly-O3G revealed that there is space in the binding pocket for the introduction of a small substituent (Figure 2), such as a methylene (O3G=) or two fluorides (O3GF2), which are weak and strong inductively electron-withdrawing groups, respectively. However, these modifications also create additional van der Waals interactions with the pocket, which by themselves can be a reason for increased affinity of the ester for the enzyme. To assess this effect, a cyclopropyl group was included (O3G∇), which was shown to fit in the binding pocket to make these additional interactions without altering the electronic properties.

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