The conformational free-energy landscape of β-D-mannopyranose: evidence for a (1)S(5) → B(2,5) → (O)S(2) catalytic itinerary in β-mannosidases.
The mechanism of glycosidic bond cleavage by glycosidases involves substrate ring distortions in the Michaelis complex that favor catalysis. Retaining β-mannosidases bind the substrate in a (1)S(5) conformation, and recent experiments have proposed an unusual substrate conformational pathway ((1)S(5) → B(2,5) → (O)S(2)) for the hydrolysis reaction. By means of Car-Parrinello metadynamics simulations, we have obtained the conformational free-energy surface (FES) of a β-d-mannopyranose molecule associated with the ideal Stoddart conformational diagram. We have found that (1)S(5) is among the most stable conformers and simultaneously is the most preactivated conformation in terms of elongation/shortening of the C1-O1/C1-O5 bonds, C1-O1 orientation, and charge development at the anomeric carbon. Analysis of the computed FES gives support to the proposed (1)S(5) → B(2,5) → (O)S(2) catalytic itinerary, showing that the degree of preactivation of the substrate in glycoside hydrolases (GHs) is related to the properties of an isolated sugar ring. We introduce a simple preactivation index integrating several structural, electronic, and energetic properties that can be used to predict the conformation of the substrate in the Michaelis complex of any GH.
Computer Simulation and Modeling Laboratory and Institut de Química Teòrica i Computacional (IQTCUB), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
Albert
A
Ardèvol
Xevi
X
Biarnés
Antoni
A
Planas
Carme
C
Rovira
D002384:Catalysis; D019277:Entropy; D006868:Hydrolysis; D008358:Mannose / Q000737:chemistry*; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D044902:beta-Mannosidase / Q000737:chemistry*
D044902:beta-Mannosidase; D008358:Mannose