R. E. Amaro, X. Cheng, I. Ivanov, D. Xu and J. A. McCammon, “Characterizing Loop Dynamics and Li- gand Recognition in Human- and Avian-Type Influ-enza Neuraminidases via Generalized Born Molecular Dynam-ics and End-Point Free Energy Calculations,” Journal of the American Chemical Society, Vol. 13, No. 13, 2009, pp. 4702-4709.

has been cited by the following article:

• TITLE: 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

  AUTHORS: Sigit Jaya Herlambang, Rosari Saleh

  KEYWORDS: Neuraminidase, Sialic Acid, Bind Stability, Functional Residues, Avian Influenza

  JOURNAL NAME: World Journal of Condensed Matter Physics, Vol.1 No.3, August 22, 2011

  ABSTRACT: 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.