PTR.tpl


 * ptr.tpl file is created for PTR, PHOSPHOTYROSINE - Rodney 02/28/2007
 * Tyrosine can become phosphorylated through the action of a tyrosine kinase. In its phosphorylated form, it can be referred to as phosphotyrosine.

Conformer Type

 * PTRBK: neutral backbone.
 * PTR01: neutral sidechain.
 * PTR-1: neutral sidechain with anionic state: -1 charge on phosphoryl group.
 * PTR-2: neutral sidechain with anionic state: -2 charge on phosphoryl group.

pKa/Em

 * pKa, PTR-1 = 5.9. Ref: Hoffmann et all, 1H and 31P NMR spectroscopy of phosphorylated model peptides, Int. J. Pept Protein Res, 1994: 44(3): 193-8
 * pKa, PTR-2,sol = 12.67.Ref: http://www.changbioscience.com/calculator/HendersonHasselbach.html

Charge

 * Charge on the phosphate group is taken from GROMACS (GROMOS87):<http://www.gromacs.org/contributed_by_users/task,cat_view/gid,37/limit,5/limitstart,0/order,name/dir,ASC/) Energetics of Nucleophile Activation in a Protein Tyrosine Phosphatase; Hansson, Nordlund, and Åqvist; Journal of Molecular Biology, 265, 118-27, 1997.