Application of sparse NMR restraints to large-scale protein structure prediction
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The protein structure prediction algorithm TOUCHSTONEX that uses sparse distance restraints derived from NMR nuclear Overhauser enhancement (NOE) data to predict protein structures at low-to-medium resolution was evaluated as follows: First, a representative benchmark set of the Protein Data Bank library consisting of 1365 proteins up to 200 residues was employed. Using N/8 simulated long-range restraints, where N is the number of residues, 1023 (75%) proteins were folded to a Ca root-mean-square deviation (RMSD) from native ,6.5A˚ in one of the top five models. The average RMSD of the models for all 1365 proteins is 5.0 A˚ . Using N/4 simulated restraints, 1206 (88%) proteins were folded to a RMSD ,6.5 A˚ and the average RMSD improved to 4.1 A˚ . Then, 69 proteins with experimental NMR data were used. Using long-range NOE-derived restraints, 47 proteins were folded to a RMSD ,6.5 A˚ with N/8 restraints and 61 proteins were folded to a RMSD ,6.5 A˚ with N/4 restraints. Thus, TOUCHSTONEX can be a tool for NMR-based rapid structure determination, as well as used in other experimental methods that can provide tertiary restraint information.