Free Energy Modelling of Substrate Distortion in the Enzyme Active Site: An Example of Influenza Neuraminidase


V. Spiwok1,2, M. Raab2, B. Králová1, I. Tvaroška2


1 Institute of Chemical Technology, Technická 3, Prague 6, 166 28, Czech Republic

2 Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences,

Dúbravska cesta 9, Bratislava, 845 38, Slovak Republic


Protein-ligand interactions are often associated with conformational changes of the molecule of protein. However, there are several interesting examples of induced fit in the molecule of ligand. For example, numerous X-ray structures of glycosidases show that the substrate (pyranose) is bound in a high-energy boat or skew-boat conformation, instead of the energetically favourable chair conformation. This substrate distortion probably facilitates the catalysis. Such distortion was also observed for a-N-acetylneuraminic acid (Neu5Ac) bound to the active site of influenza neuraminidase (sialidase).

Stabilization of the boat conformation of Neu5Ac in the active site of neuraminidase was studied using molecular dynamics simulation and metadynamics.1 The results allowed us to predict thermodynamics and kinetics of the studied conformational change in a good agreement with available experimental data. We show that the distortion is likely to be stabilized by the conserved arginine cluster, but also by the “150-loop”. This loop (mainly Asp151) has been proposed to play important role in catalysis, but, as far as our knowledge goes, its involvement in substrate distortion has not yet been studied. The results help to elucidate molecular mechanism of the reaction catalyzed by this medicinally important enzyme.


1.     Laio A., Parrinello M., Proc. Natl. Acad. Sci. USA, 99, (2002) 12562.



This investigation was supported by the Czech Ministry of Education, Youth and Sports (MSM6046137305). Computational resources were funded by the Science and Technology Assistance Agency, Slovakia, under the Contract APVV-0607-07 and the Centres of Excellence program of the Slovak Academy of Sciences (COMCHEM, Contract No. II/1/2007).