The Comparison of Substrate Stability in Neuraminidase Type 2 (N2) Active Site between A/Tokyo/3/67 and A/Pennsylvania/10218/84 with Heating Dynamics Simulation — Oak Academic Publishing
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The Comparison of Substrate Stability in Neuraminidase Type 2 (N2) Active Site between A/Tokyo/3/67 and A/Pennsylvania/10218/84 with Heating Dynamics Simulation
Departement of Physics, Mathematics and Science Faculty, University of Indonesia, Depok, Indonesia 16424
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1 Departement of Physics, Mathematics and Science Faculty, University of Indonesia, Depok, Indonesia 16424
A molecular dynamics simulation of two neuraminidase-sialic acid (NA-SA) complexes show a difference of the level of stability between sialic acid and neuraminidases that originated from viruses A/Tokyo/3/67 (Structure A) dan A/Pennsylvania/10218/84 (Structure B). Analyses of sialic acid RMSD and the change of torsional angles suggest that the sialic acid in Structure A is much more twisted and able to be influenced more by the binding of the neuraminidase functional residues than Structure B. Moreover, analyses upon hydrogen bond occupancy and binding free energy of both complexes showed that Structure A had more stable hydrogen bonds and each complex’s binding free energy were calculated to be –1.37 kcal/mol and 17.97 kcal/mol for Structure A and Structure B, respectively, further suggesting stability more dominant in Structure A than Structure B. Overall, Structure A has a more stable enzyme-substrate than Structure B.
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