Using quantum molecular simulation techniques, researchers at the group of Quantum Simulation of Biological Processes (SQPBIO) of the Computer Simulation and Modelling Laboratory (Co.S.Mo.LAB) –located at the Barcelona Science Park (PCB)- have cracked the mechanism of glycosidic bond formation in glycosyltransferases, the enzymes responsible for the structure of many carbohydrates. The study appears this week in the Angewandte Chemie (doi:10.1002/anie.201104623) and it has been classified as VIP («Very Important Paper»).

The work was led by Carme Rovira, ICREA Research Professor at the PCB and principal investigator of the group of Quantum Simulation of Biological Processes, with the collaboration of Albert Ardèvol, a PhD student working in the same group. Both researchers are also members of the Institute of Theoretical Chemistry (IQTC) of the University of Barcelona. The simulations were performed in the MareNostrum supercomputer of the Barcelona Supercomputing Center (BSC).

The glycosidic bond is a type of covalent bond that joins two monosaccharides to form different carbohydrates such as cellulose, starch or glycogen. Most glycosidic bonds are synthesized in nature from sugars that are activated by a cofactor (mostly, a nucleotide). The enzymes responsible for this action are glycosyltransferases, which form the glycosidic bond by transferring a sugar ring from a donor molecule (an activated sugar) to an acceptor molecule (typically another sugar ring).

These enzymes can operate with retention or inversion of the configuration of the anomeric carbon of the glycosidic bond they form. The mechanism of inverting glycosyltransferases is well known, but the mechanism of retaining glycosyltransferases has remained one of the most puzzling aspects in the field of glycobiology.

It had been proposed that the enzyme plays an active role in the mechanism, via the formation of a chemical bond with the donor sugar. Still, the lack of clear experimental evidence led scientists to think of a “front-face” type mechanism, extremely unusual and with limited chemical precedence. In this mechanism, the reaction takes place on a single “face” of the sugar. The front-face mechanism has been surrounded by much controversy, since in principle it implies that two covalent bonds are forming and breaking, respectively, in the same region of space.

“Now, our study demonstrates that the “front-face” type mechanism is feasible thanks to the formation of a positively charged species (an oxocarbenium ion) with an extremely short half-life that moves quickly from the donor to the acceptor. Contrary to what was thought, therefore, the front-face type mechanism does not imply a high energy, thus very unstable, transition state,”says Carme Rovira.

The modelled enzyme is glycosyltransferase trehalose-6-phosphate synthase (OtsA), which participates in the final synthesis of trehalose, a disaccharide of great importance in nature. Given their absence in mammalian biology, trehalose synthesising and processing enzymes offer attractive inhibition targets.

Using ab initio molecular dynamics (based on quantum chemistry), Ardèvol and Rovira obtained the complete molecular mechanism of the reaction of glycosidic bond formation and were able to demonstrate that OtsA follows a front-face type mechanism.

“Glycosyltransferases are responsible for the structure of many carbohydrates and, therefore, the knowledge of their mechanism of action will help to modify their function, thereby improving the synthesis of known carbohydrates and new structures. The knowledge of their molecular mechanism will also contribute to the design of inhibitors for those GTs that are involved in infectious diseases, “says Carme Rovira.

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