Contributors

John W Craft Jr
Glen Legge
Tel: (713) 743 8380
Fax: (713) 743 2636
University of Houston
Department of Biology and Biochemistry
353 SR2
Houston, Texas 77204-5001
USA

Reference

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.

Keywords: AMBER, phosphorylation, phosphoserine, phosphothreonine, and phosphotyrosine

Comments

AMBER has many files that are required to be modified to implement the phoshorylated residues into a structure. First PDB files may need to be converted into AMBER nomenclature and hydrogen atoms added. This is done using the utility protonate which requires PROTON_INFO.

The construction of the prmtop file is done by the AMBER utility leap. We use a leaprc file the contains the directives for the leap program. The new library is appended to the internal datastructures of the program by the directive, loadOff amber_sep.lib.

Finally a MASTER.RST file is constructed from that concatenation of files generated by makeDIST_RST, makeANG_RST, and makeCHIR_RST. The program makeANG_RST uses the new.map and tors.lib databases.

A set of MATLAB scripts are also provided for others wanting to transform PDB files of other modified amino acids. Details are provided in the overview and README files.