Publications [#235097] of Weitao Yang

Journal Articles
  1. Lewis, JP; Jr, CWC; Hermans, J; Pan, W; Lee, T-S; Yang, W, Active species for the ground-state complex of cytidine deaminase: A linear-scaling quantum mechanical investigation, Journal of the American Chemical Society, vol. 120 no. 22 (1998), pp. 5407-5410 [doi] .

    We present results of large-scale (1330 atoms) linear-scaling quantum mechanical semiempirical (PM3) simulations done to optimize geometries surrounding the active site within the enzyme cytidine deaminase. We make a strong prediction about the structure of the active site for the active species, based on the energetics of the calculated structures and comparisons to X-ray crystallographic data. The lowest energy structure indicates that Zn-OH- is the active species formed prior to nucleophilic attack of the ligand, that the active species of Glu-104 is with Oε2 protonated and hydrogen-bonded with N3 of the ligand, and that the C4 and OH- atoms are significantly closer than is permitted by their van der Waals radii. In addition, we predict structures corresponding to the low-pH and high-pH states in the active site of the enzyme.