Improving the efficiency of protein structure determination from NMR

Comprehensive computational experiments were performed to evaluate efficiency of the newly proposed COMBINE procedure on protein structure calculations from NMR data. This procedure is intended to combine merits of the previously developed FISINOE method with the DIANA program, widely used for NMR structure calculations. The new version of the FISINOE program, FISINOE-3, was developed to determine local conformations of proteins consistent with short-range NMR data (intraresidue and sequential distance constraints and coupling constants). For each residue, the program determines the allowed ranges of φ, ψ and χ₁ torsion angles consistent with the NMR data. The benchmark calculations were carried out on three proteins: bovine pancreatic trypsin inhibitor, crambin and avian pancreatic polypeptide. The results of the calculations obtained by the COMBINE protocol were compared with the results obtained by the STANDARD run of the DIANA program. The COMBINE procedure allowed one to significantly narrow ranges of the dihedral angle constraints before the structure calculations that, in turn, resulted in more stereospecific assignments. The numbers of (SCH₂ groups unambiguously assigned using the COMBINE procedure were significantly greater in comparison with those assigned by the STANDARD protocol. For all three proteins, the use of the COMBINE procedure almost doubled the numbers of unambiguously assigned (SCH₂ groups in comparison with STANDARD. The computational experiments clearly showed that the use of allowed ranges for torsion angles obtained by the COMBINE procedure as input data for the DIANA program provides a higher precision and accuracy of 3D protein structures reproduced from NMR constraints. The COMBINE procedure may be incorporated into any protocol using as input data the allowed ranges of torsion angles consistent with a given set of NMR constraints. Since the COMBINE procedure proved to be effective, reliable and robust, it may be recommended for general use in 3D structure determination of proteins and peptides from NMR data.