A Peptide Dendrimer Enzyme Model with a Single Catalytic Site at the Core

Abstract

Catalytic esterase peptide dendrimers with a core active site were discovered by functional screening of a 65,536-member combinatorial library of third-generation peptide dendrimers using fluorogenic 1-acyloxypyrene-3,6,8-trisulfonates as substrates. In the best catalyst, RMG3, ((AcTyrThr)(8)(DapTrpGly)(4)(DapArgSerGly)(2)DapHisSerNH2), ester hydrolysis is catalyzed by a single catalytic histidine residue at the dendrimer core. A pair of arginine residues in the first-generation branch assists substrate binding. The catalytic proficiency of dendrimer RMG3 (kcat/KM = 860 M(-1) min(-1) at pH 6.9) per catalytic site is comparable to that of the multivalent esterase dendrimer A3 ((AcHisSer)(8)(DapHisSer)(4)(DapHisSer)2DapHisSerNH2) which has fifteen histidines and five catalytic sites (Delort, E. et al. J. Am. Chem. Soc. 2004, 126, 15642-15643). Remarkably, catalysis in the single site dendrimer RMG3 is enhanced by the outer dendritic branches consisting of aromatic amino acids. These interactions take place in a relatively compact conformation similar to a molten globule protein as demonstrated by diffusion NMR. In another dendrimer, HG3 ((AcIlePro)(8)(DapIleThr)(4)(DapHisAla)(2)DapHisLeuNH2) by contrast, catalysis by a core of three histidine residues is unaffected by the outer dendritic layers. Dendrimer HG3 or its core HG1 exhibit comparable activity to the first-generation dendrimer A1 ((AcHisSer)(2)DapHisSerNH2). The compactness of dendrimer HG3 in solution is close to that a denatured peptide. These experiments document the first esterase peptide dendrimer enzyme models with a single catalytic site and suggest a possible relationship between packing and catalysis in these systems.

Glycopeptide dendrimers as Pseudomonas aeruginosa biofilm inhibitors

“…Although the peptide dendrimer sequence space is much smaller than that of a real protein, the dendritic topology avoids the necessity of folding by forcing the peptide dendrimer to adopt a globular structure. The dendritic architecture results in disordered conformations resembling the molten globule state of proteins, [40][41][42] with a dynamic tertiary structure containing few native-like secondary structure elements such as a-helices and b-sheets. 43 In contrast to proteins, peptide dendrimers are entirely stable towards denaturation.…”

Proteolysis of Peptide Dendrimers

“…[9,[10][11][12][13] Structurally, peptide dendrimers behave as molten globules in aqueous solution. [14] Contrary to folded proteins, however, they cannot be denatured to a linear disordered state; this suggests that they might be resistant to proteolytic degradation by blocking access of the protease to possible cleavage sites. Indeed multiple antigenic peptides, which are synthetic linear peptides attached to a dendritic polylysine core, have been reported to be resistant to proteolytic degradation.…”

“…We have shown previously with the example of esterase-active dendrimers that this type of third generation dendrimer can be hydrophobically collapsed, and that their degree of compaction is comparable to molten globule, and sometimes, fully-folded proteins; this suggests that such hydrophobically collapsed dendrimers might be resistant to proteolysis. [14] However, while these dendrimers were much less reactive than the second generation dendrimers above, quantitative proteolysis could be obtained when using 50 mg mL À1 of either trypsin or a-chymotrypsin. Specific cleavage was confirmed in the case of trypsin by identification of the fragments by MS, which showed that all arginine cleavage sites had reacted ( Table 2).…”

“…) and other peptide dendrimers, such as the esterase models [14] RG1-RG3 and RMG1-RMG3 (about 2.2-3.0 3 mol g À1 ; Table 4). By contrast denatured peptides and proteins occupy a much larger volume per unit of M W (about 4-12 3 mol g À1 ).…”

Synthesis of dendrimer‐type chiral stationary phases based on the selector of (1S,2R)‐(+)‐2‐Amino‐1,2‐diphenylethanol derivate and their enantioseparation evaluation by HPLC

“…1,2 Dendrimers are monodisperse oligomers and polymers usually with special function. [3][4][5] They are usually related to the fields of catalysis, [6][7][8][9] drug delivery, [10][11][12][13] liquid crystalline materials 14 and contrast media for clinic diagnosis. 15,16 In a few reported works, dendrimers are used in chromatography.…”