A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI fromStreptococcus mutans

Abstract

In this work, QM/MM calculations were employed to examine the catalytic mechanism of the retaining glucosyltransferase GTF-SI enzyme, which participates in the process of caries formation. Our goal was to characterize, with atomistic details, the mechanism of sucrose hydrolysis and the catalytic factors that modulate this reaction. Our results suggest a concerted mechanism for sucrose hydrolysis in which the first event corresponds to the glycosidic bond breakage assisted by Glu515, followed by the nucleophilic attack of Asp477, leading to the formation of the Covalent Glycosyl Enzyme (CGE) intermediate. A novel conformational itinerary of the glucosyl moiety along the reaction mechanism was identified: 2H3 → 2H3-E3 → 4C1, and the calculated energy barrier is 16.4 kcal mol-1, which is in good agreement with experimental evidence showing a major contribution coming from the glycosidic bond breakage. Our calculations also revealed that Arg475 and Asp588 play a critical role as TS-stabilizers by electrostatic and charge transfer mechanisms, respectively. This is the first report dealing with the specific features of the mechanism and catalytic residues involved in GTF-SI hydrolysis of sucrose, which is a matter of relevance in enzyme catalysis and could be valuable to aid the design of novel and specific inhibitors targeting GTF-SI.

Modulation of glucan‐enzyme interactions by domain V in GTF‐SI from Streptococcus mutans

“…On the other hand, the flexibility of the protein residues belonging to the catalytic site (Asp477, Arg475, Asp588, and Glu515 according to 3AIE residue numbering) resulted in almost no alteration upon the incorporation of domain V, thus indicating that this protein region is not critical for determining the active conformation of the catalytic center. These results indicate that, despite the relevance of domain V for the enzymatic performance of GTF‐SI, the presence of this domain should have a minor influence on the intrinsic catalytic parameters of this enzyme, which can be examined using reduced enzymatic models such as in previously reported Quantum Mechanics/Molecular Mechanics (QM/MM) approaches …”

“…Mean square root of the deviation (RMSD) trajectory analysis for GTF and GTF-V systems was carried out using the mdlovofit 20 Mechanics/Molecular Mechanics (QM/MM) approaches. 21,22 A different result was obtained for a protein region located in the neighborhood of the catalytic site, namely the α4 0 -loop-α4 00 motif, which has been recognized as a relevant segment for GTF-SI activity. 5,23 This motif is composed of the protein residues 592-627 according to the amino acid numbering of GTF-SI in the PDB code 3AIE.…”

Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective

“…Jimenez and co-workers-for example-used QM/MM simulations for studying the catalytic mechanism of the retaining glucosyltransferase GTF-SI enzyme that plays a role in the caries formation processes. 99 Ramos and co-workers described the pathway-in a mechanistic way-of human α-glucosidase maltase-glucoamylase via QM/MM simulations. 99 This was an important study because the enormous con- Boltzmann Surface Area calculations.…”

“…99 Ramos and co-workers described the pathway-in a mechanistic way-of human α-glucosidase maltase-glucoamylase via QM/MM simulations. 99 This was an important study because the enormous con- Boltzmann Surface Area calculations. The QM part was treated using M06-L using the LACVP* basis set at the DFT level.…”

Ursolic Acid Targets Glucosyltransferase and Inhibits Its Activity to Prevent Streptococcus mutans Biofilm Formation

“…S. mutans secretes three types of glucosyltransferases (GTFs), namely, GTF-I (also known as GtfB), GTF-SI (GtfC), and GTF-S (GtfD; Bowen and Koo, 2011 ). These GTFs can use dietary sucrose to synthesize extracellular polysaccharides (EPSs), and EPSs are the virulence determinants of cariogenic biofilms ( Tamesada et al, 2004 ; Bowen and Koo, 2011 ; Jaña et al, 2018 ). GTF-I and GTF-SI catalyze mainly the synthesis of water-insoluble glucans, and GTF-S produces mainly water-soluble glucans ( Monchois et al, 1999 ; Bowen et al, 2018 ).…”