J. Craft, G. Legge
University of Houston
Craft, J.W. and Legge, G.B.,
Journal of Biomolecular NMR 2005 33, 15-24
An AMBER/DYANA/MOLMOL Phosphorylated Amino Acid Library Set and
Incorporation into NMR Structure Calculations
Protein structure determination using Nuclear Magnetic Resonance (NMR) requires the use of molecular dynamics programs that incorporate both NMR experimental and implicit atomic data. Atomic parameters for each amino acid type are encoded in libraries used by structure calculation programs such as DYANA and AMBER. However, only a few non-standard amino acid library sets are included in these programs or the molecular visualization program MOLMOL. Our laboratory is calculating the phosphorylated and non-phosphorylated states of peptides and proteins using NMR methods. To calculate chemically correct structures, we have extended the available molecular libraries for these programs to include the modified amino acids phosphoserine, phosphothreonine, and phosphotyrosine.
Localized charge sums along the side chain were estimated to minimize
the deviations from similar (analogous) charged amino acid residues
like aspartic acid while maintaining backbone charges consistent with
the AMBER library and the phenyl moiety.
Note that no FRCMOD file is required as all non-electrostatic parameters exist in parm94.dat.
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