Researchers from the Quantum Simulation of Biological Processes Research Group (SQPBIO), Department of Chemistry, University of Barcelona (UB) - located at the Barcelona Science Park (PCB) - in collaboration with biochemical and structural biology groups from the UK, France and Australia, have identified important mechanistic aspects of of the enzymes that trim carbohydrates attached to proteins. The study has been published in the current issue of Angewandte Chemie (DOI: 10.1002/anie.201205338), and has been classified as a VIP ("Very Important Paper"). Only 5% of papers published in Angew. Chem. receive this distinction.

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The work was directed by Carme Rovira-ICREA research professor at the UB, principal investigator of Quantum Simulation of Biological Processes and member of the Institute of Theoretical Chemistry (IQTC) of the UB- and by Gideon Davies, Professor at University of York (UK). Researchers from the IQTC, Javier Iglesias-Fernandez, a predoctorate student at SQPBIO and Albert Ardèvol, a former member of the group, also participated in the study. The simulations were carried out at the MareNostrum supercomputer of the Barcelona Supercomputing Center (BSC).

α-mannosidase enzymes are responsible for “trimming” and / or rearranging certain carbohydrates attached to proteins. These carbohydrates have important roles in carbohydrate recognition processes and cell signaling. They also play roles in the degradation of misfolded proteins as part of the protein folding quality control apparatus. The alteration, deficiency or excess of any of these carbohydrates, is directly related to certain diseases such as tumors or lysosomal diseases.

The investigated enzyme is the one that breaks the covalent bond between two units of the α-mannose monosaccharide in carbohydrates of the Man9GlcNAc2 formula (Man = mannose, GLC = glucose, GlcNAc = N-acetylglucosamine). Using structures of the carbohydrate-enzyme complex, determined to atomic resolution, and quantum molecular dynamics simulations, the researchers have captured the change in shape of the carbohydrate during the enzymatic reaction. The results also show that the carbohydrate completely loses its freedom of movement when it is inside the enzyme (as a prisoner handcuffed hands and feet) so that only two conformations are possible. This is a key aspect to understand catalysis by carbohydrate-degrading enzymes in general at a molecular level.

The knowledge of the structure of carbohydrates during the enzymatic reaction (in particular, its conformation in the transition state or state of highest energy) is important for the design of molecules that mimic this structure (transition state mimics) and that could block the enzyme activity when it is not working properly.