Construction of a full three-dimensional model of the transpeptidase domain of Streptococcus pneumoniae PBP2x starting from its C-alpha-atom coordinates

A new method is described for generating all-atom protein structures from C -alpha-atom information. The method, which combines both local structural t race alignments and comparative side chain modeling with ab initio side cha in modeling, makes use of both the virtual-bond and the dipole-path methods . Provided that 3D structures of structurally and functionally related prot eins exist, the method presented here is highly suitable for generating all -atom coordinates of partly solved, low-resolution crystal structures. Part icularly the active site region can be modeled accurately with this procedu re, which enables investigation of the binding modes of different classes o f ligands with molecular dynamics simulations. The method is applied to the trace of Streptococcus pneumoniae, in order to construct an all-atom struc ture of the transpeptidase domain. Since after generation of full coordinat es of the transpeptidase domain the structure had been solved to 2.4 Angstr om resolution, new X-ray coordinates for the worst modeled loop (residues T 370 to M386; 17 out of a total number of 351 residues constituting the tran speptidase domain) were incorporated, as kindly provided by Dr. Dideberg. T he structure was relaxed with molecular dynamics simulations and simulated annealing methods. The RMS deviation between the 144 aligned C-alpha-atoms and the corresponding ones in the originally solved 3.5 Angstrom resolution crystal structure was 0.98. The 351 C-alpha-atoms of the whole transpeptid ase domain of the final model showed an RMS deviation of 1.58. The Ramachan dran plot showed that 79.3% of the residues are in the most favored regions , with only 1.0% occurring in disallowed regions. The model presented here can be used to investigate the three-dimensional influences of mutations ar ound the active site of PBP2x.