3D structure of bovine pancreatic ribonuclease A in aqueous solution: an approach to tertiary structure determination from a small basis of 1H NMR NOE correlations

Abstract

A method is proposed to generate initial structures in cases where the distance geometry method may fail, such as when the set of 1H NMR NOE-based distance constraints is small in relation to the size of the protein. The method introduces an initial correlation between the phi and psi backbone angles (based on empirical observations) which is relaxed in later stages of the calculation. The obtained initial structures are refined by well-established methods of energy minimization and restrained molecular dynamics. The method is applied to determine the solution structure of Ribonuclease A (124 residues) from a NOE basis consisting of 467 NOE cross-correlations (97 intra-residue, 206 sequential, 23 medium-range and 141 long-range) obtained at 360 MHz. The global shape and backbone overall fold of the eight final refined structures are close to those shown by the crystal structure. A meaningful difference in the positioning of the catalytically important His119 side chain in the solution and crystal structures has been detected.