Do zwitterionic species exist in the non-enzymatic peptide bond formation?

Abstract

The use of proper computational methods and models has allowed answering the controversial question of whether zwitterionic species exist in the mechanism of peptide bond synthesis in aqueous solution. In fact, the different conformations of zwitterionic species open the door to different mechanistic paths.The peptide bond synthesis mechanism in ribosomes has attracted much attention in the past years. In order to get information on this problem, aminolysis of esters in aqueous solution has been the subject of many experimental and theoretical studies. The main reason for this interest comes from the hypothesis that similar mechanisms are involved in both media. Experimental studies based on linear free-energy relationships 1 and isotope substitution effects 2 in solution support a stepwise mechanism with participation of different kinds of intermediates, ranging from anionic, cationic, neutral and zwitterionic species. Based on theoretical studies, 3-5 three different mechanisms have been proposed: (1) a concerted mechanism in which the nucleophilic attack on the amino group, the C-O bond cleavage and the proton transfer take place simultaneously; (2) a stepwise mechanism through a neutral intermediate; and (3) a stepwise mechanism through a zwitterionic intermediate. The latter mechanism has been the subject of controversy since even the presence of this intermediate has been questioned. Nevertheless, theoretical studies using a reduced number of water molecules to describe the solvent, or by mixed explicit-polarizable continuum models (PCM), despite their limitations, 6 have supported the existence of this intermediate. [7][8][9] Warshel and coworkers located a zwitterionic intermediate in the catalyzed methanolysis of formamide (formally the reverse reaction of the one studied in the present manuscript) by combined ab initio/Langevin dipole calculations, 10 and more recently the solute electron density model (SMD) 11 has also been used to stabilize zwitterionic species. 12 The present communication is focused on the existence and relevance of the zwitterionic species in the aminolysis of esters in solution within a realistic molecular model similar to the natural substrate used by ribosomes, as shown in Scheme 1. The model of the substrate in our hybrid QM/MM calculations includes all the atoms involved in the different proposed mechanisms. It is important to point out that previous theoretical studies in solution have been performed with simpler molecular models ignoring, for instance, the constraint of the ribose ring that can govern the role of the hydroxyl group bound to C2 0 .The substrate has been treated by semiempirical AM1 13 hamiltonian and by means of the M06-2X functional developed by Truhlar's group 14 with the standard 6-31+G(d,p) basis set. The full molecule described quantum mechanically has been embedded in a cubic box of water molecules (100 Â 80 Â 80 Å 3 ) treated by the TIP3P 15 force field, as implemented in the fDYNAMO library. 16 Periodic boundary conditions were applied and a switched...

Peptide Bond Formation Mechanism Catalyzed by Ribosome

“…It is important to point out that this structure does not correspond to a stationary point on the free energy profiles for the reaction obtained in solution or in the ribosome. As previously described, the formation of this transient zwitterionic structure in solution was associated with a shoulder on the free energy profile, 24,25 which has not been observed in the case of the ribosome. Geometries of these zwitterionic structures, ZW, are shown in Figure 3, while atomic charges on key atoms are listed in Table 1.…”

Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease

“…A transient but relevant behavior of a zwitterion species was already observed in the inverse process, the peptide bond formation, catalyzed by ribosome, 108 and also in the counterpart non-enzymatic reaction in solution. 109, 110 …”

Theoretical Study of the Mechanism of Ribosomal Peptide Bond Formation Using the ONIOM Method

“…Although the role of the 2′-OH group of A76 of peptidyl-tRNA is debatable, [33][34][35][36][37] we adopted a substrate-assisted catalysis model in which the 2′-OH group of A76 catalyzes peptide bond formation, 37) since this is consistent with experimental data and calculated models from previous mechanistic studies. 8,9,[12][13][14][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31]33,34) The optimized geometries of TS1 and TS2 are shown in Fig. 3.…”

“…4), which are lower than the values obtained in our previous study (24.3 and 51.9 kcal mol −1 , respectively). 23) This decreased energy barrier indicates that intermolecular interactions such as electrostatic and van der Waals interactions between substrates and the PTC environment stabilize the transition states, especially TS2. Although it is very difficult to quantitatively evaluate the effect of the PTC environment on the reaction mechanism in the present calculations, Figs.…”

“…18) Quantum chemical calculations have been used to study both stepwise and concerted mechanisms. [20][21][22][23][24][25][26][27][28][29][30][31] In one study of systems containing 44-56 atoms of the PTC analyzed using the M06-2X/6-311 + G(d,p) level of theory, C-N bond formation and C-O bond cleavage were accompanied by proton transfer of the NH 2 group, 2′-OH group of A76, and water molecules in the transition states (proton-shuttle mechanism); these authors showed that a stepwise reaction was favored over a concerted one and that the 2′-OH group of rRNA A2451 in the active site of the ribosome stabilized the transition states through hydrogen bonding. 22) In a previous study, we demonstrated the stepwise mechanism of the peptidyl transfer reaction in a ribosome system consisting of 2354 atoms using the ONIOM method 23) (Fig.…”