Contributors

N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht
Bioinformatik, Institut f. Biochemie,
Friedrich-Alexander-Universitat Erlangen-Nurnberg, Germany
www: http://www.biochem.uni-erlangen.de
and
Computer Chemie Centrum,
Friedrich-Alexander-Universitat Erlangen-Nurnberg, Germany
www: http://www.chemie.uni-erlangen.de/ccc

References

N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht
J. Mol. Model. 2006, 12, 281-289.
AMBER force field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine and phosphohistidine
We report a consistent set of AMBER force-field parameters for the most common phosphorylated amino acids, phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine in different protonation states. The calculation of atomic charges followed the original restrained electrostatic potential fitting procedure used to determine the charges for the parm94/99 parameter set, taking alpha-helical and beta-strand conformations of the corresponding ACE-/NME-capped model peptide backbone into account. Missing force-field parameters were taken directly from the general AMBER force field (gaff) and the parm99 data set with minor modifications, or were newly generated based on ab initio calculations for model systems. Final parameters were validated by geometry optimizations and molecular-dynamics simulations. Template libraries for the phosphorylated amino acids in Leap format and corresponding frcmod parameter files are made available.

Comments

H1D.off / frcmod_h1d : Phosphohistidine with single protonated phosphate group, phosphorylated at ND1, HIS(ND1)-PO2(OH)
H2D.off / frcmod_h2d : Phosphohistidine with unprotonated phosphate group, phosphorylated at ND1, HIS(ND1)-PO3
H1E.off / frcmod_h1e : Phosphohistidine with single protonated phosphate group, phosphorylated at NE2, HIS(NE2)-PO2(OH)
H2E.off / frcmod_h2e : Phosphohistidine with unprotonated phosphate group, phosphorylated at NE2, HIS(NE2)-PO3
S1P.off / frcmod_s1p : Phosphoserine with single protonated phosphate group, SER-PO2(OH)
S2P.off / frcmod_s2p : Phosphoserine with unprotonated phosphate group, SER-PO3
T1P.off / frcmod_t1p : Phosphothreonine with single protonated phosphate group, THR-PO2(OH)
T2P.off / frcmod_t2p : Phosphothreonine with unprotonated phosphate group, THR-PO3
Y1P.off / frcmod_y1p : Phosphotyrosine with single protonated phosphate group, TYR-PO2(OH)
Y2P.off / frcmod_y2p : Phosphotyrosine with unprotonated phosphate group, TYR-PO3

We developed AMBER force field parameters for the most common phospho-amino acids in two different protonation states.

All new parameters were calculated according to procedures used for the generation of the parm94/99 parameters and recommended in the AMBER mannual. RESP charges were generated by performing a three stage RESP fit on two HF/6-31G* optimized structures representing the alpha-helical and beta-strand conformations of the phospho-amino acids. Missing bond and torsion parameters were developed by fitting AMBER energies onto ab initio (GAUSSIAN) calculated ones.

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Last modified Wed Jun 22 16:31:51 BST 2005